Small molecules

ABSTRACT

Compounds having the general structure A-L-B are presented wherein A and B are independently an E3 ubiquitin ligase protein binding ligand compound of formula 1A or 1B. Pharmaceutical compositions comprising these compounds and methods of use are also presented.

FIELD OF THE INVENTION

This invention relates to small molecule E3 ubiquitin ligase proteinbinding ligand compounds, and to their utility in PROteolysis TargetedChimeras (PROTACs), as well as processes for the preparation thereof,and use in medicine. This invention particularly relates to PROTACscapable of inducing auto-ubiquitination of E3 ubiquitin ligases andtriggering their subsequent proteasomal degradation.

BACKGROUND OF THE INVENTION

E3 ubiquitin ligases are emerging as attractive targets forsmall-molecule modulation and drug discovery. E3s bring a substrateprotein and ubiquitin in close proximity to each other to catalyze thetransfer of a ubiquitin molecule to the substrate. Substrateubiquitination can trigger different cellular outcomes, of which one ofthe best characterized is poly-ubiquitination and subsequent proteasomaldegradation. The human genome comprises >600 predicted E3 ligases thatplay important roles in normal cellular physiology and disease states,making them attractive targets for inhibitor discovery. However, E3ligases do not comprise deep and “druggable” active sites for binding tosmall molecules. Blockade of E3 ligase activity therefore requirestargeting of protein-protein interactions (PPIs), and the oftenextended, flat and solvent-exposed PPI surfaces make it a challenge fordrug design. Only a few potent inhibitors have been developed to date,mostly compounds that bind to the E3 substrate recognition site, forexample MDM2, inhibitor of apoptosis proteins (IAPs), the vonHippel-Lindau (VHL) ligase,¹⁻³ and KEAP1. Inhibitors of E3:substrateinteraction can exhibit a discrepancy in effective concentrationsbetween biophysical binding and cellular efficacy,³ due to competitionfrom high-affinity endogenous substrates that markedly increase theircellular concentration as a consequence of the inhibition. This poseslimitations, such as the need to use high inhibitor concentrations,which can lead to off-target effects and cytotoxicity, and incompleteblockade of enzyme activity. Moreover, E3 ligases are multi-domain andmulti-subunit enzymes, and targeting an individual binding site leavesother scaffold scaffolding regions untouched and other interactionsfunctional. As a result, E3 ligase inhibition may be ineffective or failto recapitulate genetic knockout or knockdown. New chemical modalitiesto target E3 ligases are therefore demanded.

E3 ligases are not merely targets for inhibition. Compounds of naturalor synthetic origin have been discovered that bind to E3 ligases andpromote the recruitment of new proteins. These interfacial compoundsinduce de novo formation of ligase-target PPIs effectively hijacking E3ubiquitination activity towards the neo-substrates, for targeted proteindegradation. One class of small molecule hijackers of E3 ligase activitycomprises monovalent compounds. These so-called “molecular glues”include the plant hormone auxin, which binds to the Cullin RING ligase(CRL) CRL1-TIR1 to target transcriptional repressor proteins of theAux/IAA family, and the immunomodulatory drugs (IMiDs) thalidomide,lenalidomide, pomalidomide and analogue CC-885, that all bind tocereblon (CRBN), a subunit of the CRL4-CRBN ligase, and redirect CRBNactivity to different substrates.⁴⁻¹⁰ More recently, the sulfonamideanti-cancer drug indisulam was found to induce degradation of thesplicing factor RBM39 via recruiting CRL4-DCAF15 activity. A distinctclass of compounds that display a similar mechanism of action arebivalent molecules called Proteolysis-Targeting Chimeras (PROTACs).PROTACs comprise of a first warhead moiety for a ligase, and a secondwarhead for a target protein, joined by a linker.¹¹ Formation of aternary complex between the PROTAC, the ligase and the target triggersproximity-induced target ubiquitination and degradation. Warhead ligandshave been used to develop potent and cell-active PROTACs recruitingdifferent ligases, including CRL2-VHL,¹²⁻¹⁵ CRL4-CRBN,¹⁶⁻²⁰ andIAPs.²¹⁻²² Amongst the targets successfully degraded by PROTACs are BETproteins Brd2, Brd3 and Brd4,^(12,14-17) FKBP,^(16,20) proteinkinases,^(13,18) amongst others^(13,21) An attractive feature of PROTACsis their sub-stoichiometric catalytic activity,¹³ which does not requirefull occupancy of the target-binding site as with conventionalinhibitors, leading to degrading concentrations that can be orders ofmagnitude lower than the inhibitory concentrations of their constitutiveparts alone. Furthermore, induced target depletion can have a moresustained cellular effect compared to target inhibition, and canovercome compensatory cellular feedback mechanisms, such as increase intarget levels. Crucially, it has been shown that PROTAC molecules canexhibit an added layer of selectivity for protein degradation beyond theintrinsic binding selectivity of the warhead ligand^(12,15,18) Ourrecent structural work with Brd4-selective PROTACs targeting CRL2-VHLrevealed that the importance of specific ligand-induced PPIs between theligase and the target, which contribute to cooperative formation ofstable and highly populated ternary complexes.¹⁵

The inventors have now found that it is possible to target E3 ligasesthemselves for ubiquitination and proteasomal degradation, using asuitably designed PROTAC. For at least some aspects the inventors havefound that a PROTAC comprising two instances of an E3 binding moiety maybe capable of forming ternary complexes in which the same E3 functionsas both ubiquitinating enzyme and neo-substrate.

SUMMARY OF THE INVENTION

According to a first aspect of the invention there is provided acompound having the structure:

A-L-B

wherein A and B are independently an E3 ubiquitin ligase protein bindingligand compound of formula 1A or 1B:

wherein L is a linking group which is directly bonded to the compound offormula 1A at R¹ or R², and/or directly bonded to the compound offormula 1B at R³ or R⁴ and wherein L is —R⁵—[O(CH₂)_(m)]_(n)—R⁶—,wherein m and n are independently 0 to 10, and R⁵ and R⁶ areindependently selected from the group: covalent bond, C1-C10 alkylene,C1-C10 polyether, or —O—;

wherein R¹ is selected from either the group: (1) a covalent bond, orC1-C5 alkylene when L is bonded to the compound of formula 1A at R¹, orthe group (2) H, NH₂, C1-C5 alkyl, or C(CN)CH₄when L is bonded to thecompound of formula 1A at R²;

wherein R², R³, and R⁴ are independently selected from the group: acovalent bond, H, NH₂, C1-C5 alkyl, C(CN)C₂H₄;

wherein X and Y are independently selected from the group: H, OH orhalogen; and

wherein R⁷ is C1-C5 alkylene,

or a pharmaceutically acceptable salt, hydrate, solvate or polymorphthereof.

Accordingly, the compound of formula A-L-B may comprise a compound ofeither formula 1A or 1B connected via the linker L to a compound ofeither formula 1A or 1B. In embodiments where A and/or B is a compoundof formula 1A, the compound of formula 1A may be connected to the linkerL via R¹ or R². In embodiments where A and/or B is a compound of formula1B, the compound of formula 1B may be connected to the linker L via R³or R⁴.

Compounds having the general formula A-L-B as described herein may bereferred to in the description below as “PROTAC-compounds”, “HOMO-PROTACcompounds” (wherein the moiety A is the same as the moiety B),“Hetero-PROTAC compounds” (wherein the moiety A is different to moietyB), or simply as “compounds of the invention”.

The inventors have surprising found that the compounds having thestructure A-L-B as defined above are able to induce degradation of E3ubiquitin ligase protein within a cell by using the E3 ubiquitinationmechanism itself. Accordingly, it suggested that the compounds ofstructure A-L-B forms a tertiary structure with two E3 ubiquitin ligaseproteins such that one E3 ubiquitin ligase protein ubiquitinates anotherE3 ubiquitin ligase protein to which it is joined by the compound ofstructure A-L-B. It is further suggested that this ubiquitination isinduced due to the enforced close proximity of the two E3 ubiquitinligase proteins in the tertiary structure formed by binding of the E3ubiquitin ligase proteins with the compounds of formula 1A or 1B.

Furthermore, it has been found that the compounds of the invention areable to initiate the degradation at sub-stoichiometric concentrations,thereby indicating that the compounds are at least partially catalysingthe degradation.

In some embodiments X may be H or halogen.

In embodiments where X is a halogen, X may be selected from F, Cl, Br,or I. For example, X may be selected from F or Cl. X may be F.

In some embodiments, Y may be OH. Typically, Y is in the “down” positionas illustrated in formula 1C below.

In embodiments where either A or B is a compound according to formula1A, A or B may have the formula 1C:

In some embodiments, A may be a compound of formula 1A and B may be acompound of formula 1A.

L may be connected to A via R¹ of formula 1A. L may be connected to Bvia R¹ of formula 1A.

Alternatively, L may be connected to A via R² of formula 1A and L may beconnected

In some embodiments, R⁵ may be a chemical bond, R⁶ may be a chemicalbond, m may be 2 and n may be 3, 4 or 5.

In some preferred embodiments, n is 5.

The compound of some embodiments may have formula 2, 3 or 4:

wherein R^(2a), R^(2b) and R^(2c) are independently selected from H,NH₂, C1-C5 alkyl, and C(CN)C₂H₄;

R^(1a), R^(1b) and R^(1c) are independently selected from H, NH₂, C1-C5alkyl, and C(CN)C₂H₄;

X¹ and X² are independently selected from H, OH, halogen;

Y¹ and Y² are independently selected from H, OH, halogen; and

m and n are independently 0 to 10.

Preferably for compounds of formula 2, 3 or 4, n is 3-5. Typically, m is1-4. Preferably, m is 2 such that the linker is formed of polyethyleneglycol subunits.

In embodiments, R^(1a), R^(1b) and R^(1c) may be independently selectedfrom C1-C5 alkyl or C(CN)C₂H₄. In further embodiments, R^(1a), R^(1b)and R^(1c) may be independently selected from C1 alkyl (i.e. methyl orMe) and C(CN)C₂H₄.

In some embodiments R^(2a), R^(2b) and R^(2c) may be H.

In some embodiments, Y¹ and Y² may be OH, X¹ and X² may be H, R^(1a),R^(1b) and R^(1c) may independently be Me or C(CN)C₂H₄ and R^(2a),R^(2b) and R^(2c) may be H.

In preferred embodiments the linker L is a linear chain of 12-20 atomsin length. The compounds of the invention have been found to be mostuseful to induce degradation of target proteins when the groups A and Bare spaced apart. Accordingly, without wishing to be bound by theory, ithas been found that a linker L being a linear chain of 12-20 atoms inlength spaces the groups A and B apart a sufficient distance to allowthem to bind to their target binding sites without interfering with oneanother, whilst at the same time ensuring that the target proteins areheld in sufficient proximity that the E3 ubiquitin ligase protein boundto either or both A and B can ubiquitinate the target protein, therebymarking that protein for subsequent degradation by the cell's machinery.

L may be a linear chain of 15-18 atoms in length. For example, L may bea linear chain of 15, 16, 17 or 18 atoms in length.

Typically, the linker chain may comprise carbon and/or oxygen atoms. Forexample, the linker chain may comprise alkylene groups and/or ethergroups and/or polyether groups.

Alternatively, the linker chain may be a peptide chain, or nucleotidechain, for example.

As used herein, the term “pharmaceutically acceptable salt” refers tothose salts of the compounds formed by the process of the presentinvention which are, within the scope of sound medical judgment,suitable for use in contact with the tissues of humans and lower animalswithout undue toxicity, irritation, allergic response and the like, andare commensurate with a reasonable benefit/risk ratio. Pharmaceuticallyacceptable salts are well known in the art. The salts can be prepared insitu during the final isolation and purification of the compounds of theinvention, or separately by reacting the free base function with asuitable organic acid. Examples of pharmaceutically acceptable saltssuitable for use herein include, but are not limited to, nontoxic acidaddition salts are salts of an amino group formed with inorganic acidssuch as hydrochloric acid, hydrobromic acid, phosphoric acid, sulfuricacid and perchloric acid or with organic acids such as acetic acid,maleic acid, tartaric acid, citric acid, succinic acid or malonic acidor by using other methods used in the art such as ion exchange.

Other pharmaceutically acceptable salts include, but are not limited to,adipate, alginate, ascorbate, aspartate, benzenesulfonate, benzoate,bisulfate, borate, butyrate, camphorate, camphorsulfonate, citrate,cyclopentanepropionate, digluconate, dodecylsulfate, ethanesulfonate,formate, fumarate, glucoheptonate, glycerophosphate, gluconate,hemisulfate, heptanoate, hexanoate, hydroiodide,2-hydroxy-ethanesulfonate, lactobionate, lactate, laurate, laurylsulfate, malate, maleate, malonate, methanesulfonate,2-naphthalenesulfonate, nicotinate, nitrate, oleate, oxalate, palmitate,pamoate, pectinate, persulfate, 3-phenylpropionate, phosphate, picrate,pivalate, propionate, stearate, succinate, sulfate, tartrate,thiocyanate, p-toluenesulfonate, undecanoate, valerate salts, and thelike. Representative alkali or alkaline earth metal salts includesodium, lithium, potassium, calcium, magnesium, and the like. Furtherpharmaceutically acceptable salts include, when appropriate, nontoxicammonium, quaternary ammonium, and amine cations formed usingcounterions such as halide, hydroxide, carbon/late, sulfate, phosphate,nitrate, alkyl having from 1 to 6 carbon atoms, sulfonate and arylsulphonate.

In a preferred aspect herein the compounds of formula I for use in thePROTAC compounds of structure A-L-B- as defined herein are representedas a defined stereoisomer. The absolute configuration of such compoundscan be determined using art-known methods such as, for example, X-raydiffraction or NMR and/or implication from starting materials of knownstereochemistry.

Pharmaceutical compositions in accordance with the invention willpreferably comprise substantially stereoisomerically pure preparationsof the indicated stereoisomer.

Pure stereoisomeric forms of the compounds and intermediates asmentioned herein are defined as isomers which are substantially free ofother enantiomeric or diastereomeric forms of the same basic molecularstructure of said compounds or intermediates. In particular, the term“stereoisomerically pure” concerns compounds or intermediates having astereoisomeric excess of at least 80% (i.e. minimum 90% of one isomerand maximum 10% of the other possible isomers) up to a stereoisomericexcess of 100% (i.e. 100% of one isomer and none of the other), more inparticular, compounds or intermediates having a stereoisomeric excess of90% up to 100%, even more in particular having a stereoisomeric excessof 94% up to 100% and most in particular having a stereoisomeric excessof 97% up to 100%. The terms “enantiomerically pure” and“diastereomerically pure” should be understood in a similar way, butthen having regard to the enantiomeric excess, and the diastereomericexcess, respectively, of the mixture in question.

Pure stereoisomeric forms of the compounds and intermediates as detailedherein may be obtained by the application of art-known procedures. Forinstance, enantiomers may be separated from each other by the selectivecrystallization of their diastereomeric salts with optically activeacids or bases. Examples thereof are tartaric acid, dibenzoyl¬tartaricacid, ditoluoyltartaric acid and camphorsulfonic acid. Alternatively,enantiomers may be separated by chromatographic techniques using chiralstationary phases. Said pure stereochemically isomeric forms may also bederived from the corresponding pure stereochemically isomeric forms ofthe appropriate starting materials, provided that the reaction occursstereo-specifically. Preferably, if a specific stereoisomer is desired,said compound is synthesized by stereospecific methods of preparation.These methods will advantageously employ enantiomerically pure startingmaterials.

The diastereomeric racemates of the compounds of formula 1A or 1B foruse in the PROTAC compounds of structure A-L-B as defined herein can beobtained separately by conventional methods. Appropriate physicalseparation methods that may advantageously be employed are, for example,selective crystallization and chromatography, e.g. columnchromatography.

According to a second aspect of the invention there is provided acompound selected from the following group:

In a preferred embodiment, the compound is selected from the group ofcompounds (7) to (13). For example, the compound may be compound (7).

The invention extends in a third aspect to a pharmaceutical compositioncomprising one or more compounds according to the first or second aspectand a pharmaceutically acceptable vehicle or diluent therefor.

PROTAC compounds of the invention can be administered as pharmaceuticalcompositions by any conventional route, in particular enterally, e.g.,orally, e.g., in the form of tablets or capsules, or parenterally, e.g.,in the form of injectable solutions or suspensions, topically, e.g., inthe form of lotions, gels, ointments or creams, or in a nasal orsuppository form. Pharmaceutical compositions comprising a PROTACcompound of the present invention in free form or in a pharmaceuticallyacceptable salt form in association with at least one pharmaceuticallyacceptable carrier or diluent can be manufactured in a conventionalmanner by mixing, granulating or coating methods. For example, oralcompositions can be tablets or gelatin capsules comprising the activeingredient together with a) diluents, e.g., lactose, dextrose, sucrose,mannitol, sorbitol, cellulose and/or glycine; b) lubricants, e.g.,silica, talcum, stearic acid, its magnesium or calcium salt and/orpolyethyleneglycol; for tablets also c) binders, e.g., magnesiumaluminum silicate, starch paste, gelatin, tragacanth, methylcellulose,sodium carboxymethylcellulose and or polyvinylpyrrolidone; if desired d)disintegrants, e.g., starches, agar, alginic acid or its sodium salt, oreffervescent mixtures; and/or e) absorbents, colorants, flavors andsweeteners. Injectable compositions can be aqueous isotonic solutions orsuspensions, and suppositories can be prepared from fatty emulsions orsuspensions. The compositions may be sterilized and/or containadjuvants, such as preserving, stabilizing, wetting or emulsifyingagents, solution promoters, salts for regulating the osmotic pressureand/or buffers. In addition, they may also contain other therapeuticallyvaluable substances. Suitable formulations for transdermal applicationsinclude an effective amount of a PROTAC compound of the presentinvention with a carrier. A carrier can include absorbablepharmacologically acceptable solvents to assist passage through the skinof the host. For example, transdermal devices are in the form of abandage comprising a backing member, a reservoir containing the compoundoptionally with carriers, optionally a rate controlling barrier todeliver the compound to the skin of the host at a controlled andpredetermined rate over a prolonged period of time, and means to securethe device to the skin. Matrix transdermal formulations may also beused. Suitable formulations for topical application, e.g., to the skinand eyes, are preferably aqueous solutions, ointments, creams or gelswell-known in the art. Such may contain solubilizers, stabilizers,tonicity enhancing agents, buffers and preservatives.

The pharmaceutical compositions of the present invention comprise atherapeutically effective amount of a PROTAC compound of the presentinvention formulated together with one or more pharmaceuticallyacceptable carriers. As used herein, the term “pharmaceuticallyacceptable carrier” means a non-toxic, inert solid, semi-solid or liquidfiller, diluent, encapsulating material or formulation auxiliary of anytype.

The pharmaceutical compositions of this invention can be administered tohumans and other animals orally, rectally, parenterally,intracisternally, intravaginally, intraperitoneally, topically (as bypowders, ointments, or drops), buccally, or as an oral or nasal spray.

Liquid dosage forms for oral administration include pharmaceuticallyacceptable emulsions, microemulsions, solutions, suspensions, syrups andelixirs. In addition to the active compounds, the liquid dosage formsmay contain inert diluents commonly used in the art such as, forexample, water or other solvents, solubilizing agents and emulsifierssuch as ethyl alcohol, isopropyl alcohol, ethyl carbonate, ethylacetate, benzyl alcohol, benzyl benzoate, propylene glycol, 1,3-butyleneglycol, dimethylformamide, oils (in particular, cottonseed, groundnut,corn, germ, olive, castor, and sesame oils), glycerol,tetrahydrofurfuryl alcohol, polyethylene glycols and fatty acid estersof sorbitan, and mixtures thereof. Besides inert diluents, the oralcompositions can also include adjuvants such as wetting agents,emulsifying and suspending agents, sweetening, flavoring, and perfumingagents.

Injectable preparations, for example, sterile injectable aqueous oroleaginous suspensions may be formulated according to the known artusing suitable dispersing or wetting agents and suspending agents. Thesterile injectable preparation may also be a sterile injectablesolution, suspension or emulsion in a nontoxic parenterally acceptablediluent or solvent, for example, as a solution in 1,3-butanediol. Amongthe acceptable vehicles and solvents that may be employed are water,Ringer's solution, U.S.P. and isotonic sodium chloride solution. Inaddition, sterile, fixed oils are conventionally employed as a solventor suspending medium. For this purpose any bland fixed oil can beemployed including synthetic mono- or diglycerides.

In addition, fatty acids such as oleic acid are used in the preparationof injectables. In order to prolong the effect of a drug, it is oftendesirable to slow the absorption of the drug from subcutaneous orintramuscular injection. This may be accomplished by the use of a liquidsuspension of crystalline or amorphous material with poor watersolubility. The rate of absorption of the drug then depends upon itsrate of dissolution which, in turn, may depend upon crystal size andcrystalline form. Alternatively, delayed absorption of a parenterallyadministered drug form is accomplished by dissolving or suspending thedrug in an oil vehicle. Compositions for rectal or vaginaladministration are preferably suppositories which can be prepared bymixing the PROTAC compounds of the invention with suitablenon-irritating excipients or carriers such as cocoa butter, polyethyleneglycol or a suppository wax which are solid at ambient temperature butliquid at body temperature and therefore melt in the rectum or vaginalcavity and release the active compound. Solid compositions of a similartype may also be employed as fillers in soft and hard-filled gelatinecapsules using such excipients as lactose or milk sugar as well as highmolecular weight polyethylene glycols and the like.

The PROTAC compounds can also be provided in micro-encapsulated formwith one or more excipients as noted above. The solid dosage forms oftablets, dragees, capsules, pills, and granules can be prepared withcoatings and shells such as enteric coatings, release controllingcoatings and other coatings well known in the pharmaceutical formulatingart. In such solid dosage forms the active compound may be admixed withat least one inert diluent such as sucrose, lactose or starch. Suchdosage forms may also comprise, as is normal practice, additionalsubstances other than inert diluents, e.g., tableting lubricants andother tableting aids such a magnesium stearate and microcrystallinecellulose. In the case of capsules, tablets and pills, the dosage formsmay also comprise buffering agents.

Dosage forms for topical or transdermal administration of a compound ofthis invention include ointments, pastes, creams, lotions, gels,powders, solutions, sprays, inhalants or patches. The active componentis admixed under sterile conditions with a pharmaceutically acceptablecarrier and any needed preservatives or buffers as may be required.Ophthalmic formulation, ear drops, eye ointments, powders and solutionsare also contemplated as being within the scope of this invention. Theointments, pastes, creams and gels may contain, in addition to an activecompound of this invention, excipients such as animal and vegetablefats, oils, waxes, paraffins, starch, tragacanth, cellulose derivatives,polyethylene glycols, silicones, bentonites, silicic acid, talc and zincoxide, or mixtures thereof.

Powders and sprays can contain, in addition to the PROTAC compounds ofthis invention, excipients such as lactose, talc, silicic acid,aluminium hydroxide, calcium silicates and polyamide powder, or mixturesof these substances. Sprays can additionally contain customarypropellants such as chlorofluorohydrocarbons. Transdermal patches havethe added advantage of providing controlled delivery of a compound tothe body. Such dosage forms can be made by dissolving or dispensing thecompound in the proper medium. Absorption enhancers can also be used toincrease the flux of the compound across the skin. The rate can becontrolled by either providing a rate controlling membrane or bydispersing the compound in a polymer matrix or gel.

In a fourth aspect, the invention provides a PROTAC compound ofstructure A-L-B as defined herein for use as a medicament.

In a fifth aspect of the invention there is provided a method of use ofa compound according to any of the first or second aspect or apharmaceutical composition according to the third aspect for thetreatment of at least one of anaemia due to chronic kidney disease²³,anaemia due to cancer chemotherapy²⁴, ischemia²⁵, ischemic reperfusioninjuries²⁶, myocardial infarction²⁷, stroke²⁷, acute lung injury²⁸,intestinal inflammation²⁹, wound healing³⁰ and post-transplantationcomplications³¹, mitochondrial respiratory chain dysfunctions³² andoncological conditions treatable by enhancing T-cell responses³³.

According to a sixth aspect of the invention there is provided a methodof regulating activity of a target protein in a subject comprisingadministering to said subject a therapeutically effective amount of acompound according to the first or second aspect, or a pharmaceuticalcomposition according to the third aspect.

The term “subject” as used herein refers to a mammal. A subjecttherefore refers to, for example, dogs, cats, horses, cows, pigs, guineapigs, and the like. Preferably the subject is a human. When the subjectis a human, the subject may also be referred to herein as a patient.

The term “therapeutically effective amount” means an amount effective totreat, cure or ameliorate a disease, condition illness or sickness.

Preferably, the target protein is an E3 ubiquitin ligase protein.Typically the E3 ubiquitin ligase protein is selected from CRL2-VHL,CRL4-CRBN. The E3 ubiquitin ligase protein may be selected from any ofthe >230 cullin RING ligases, for example CRL1-Skp2, CRL1-bTrCP,CRL1-Fbw, CRL1-Fbxo, CRL1-Fbxl, CRL2-LRR1, CRL2-FEM1, CRL3-Keap1,CRL3-KLHL, CRL3-SPOP, CRL4-DDB2, CRL4-DCAF, CRL4-CSA, CRL4-CDT2,CRL5-SOCS, CRL5-ASB. Other E3 ubiquitin ligase proteins may be selectedfrom MDM2, c-Cbl, APC-C, FANCL, UBE3A, UBE3B, UBE3C, UBE3D, Parkin,SIAH, XIAP, UHRF1, TRAF6, PELI2, RNF2, RNF4 amongst others.

Preferred and optional features of the first to sixth aspects may bepreferred and optional features of the other of the first to sixthaspects as appropriate.

BRIEF DESCRIPTION OF THE FIGURES

Embodiments of the present invention will now be described, by way ofnon-limiting example, with reference to the accompanying drawings.

FIG. 1: (a) Crystal structures of VHL in complex with VH298 (PDB code5LLI). VHL is shown in surface representation and the bound ligand assticks representation. (b) Chemical structure of VHL inhibitors VH032and VH298.

FIG. 2: General chemical structure and design of Homo-PROTACs compounds.Linkage sites at acetyl and phenyl group are indicated.

FIG. 3: Synthesis of Homo-PROTACs compounds symmetric from acetyl groupCM09, CM10, CM11 and negative control compound CMP98.

FIG. 4: Synthesis of negative control Homo-PROTAC compound CMP99 withcis-trans configuration.

FIG. 5: Synthesis of VHL binding moieties 17 and 18

FIG. 6: Synthesis of Homo-PROTACs CMP106 and CMP108 symmetricallyderivatized from the phenyl group.

FIG. 7: Synthesis of asymmetric Homo-PROTACs CMP112 and CMP113.

FIG. 8: Biological evaluation of HOMO-PROTACs. (a) HeLa cells weretreated with 0.1% DMSO, VH032 (150 μM) and 1 μM of the indicatedcompounds for 10 h. Abundance of individual proteins was analyzed byWestern blotting using corresponding specific antibodies accordinglyafter SDS-PAGE. (b) Different cells lines were treated with si-RNAtargeting VHL proteins or negative control si-RNA (for 48 h), as well aswith CM11 (1 μM) or 0.1% v/v DMSO for 10 h.

FIG. 9: HeLa cells were treated with increasing concentration ofHOMO-PROTAC CM11 for 4 h or 24 h.

FIG. 10: Time-course immunoblots of lysates from HeLa cells subjected to0.1% DMSO, CoCl2 (100 mM), IOX2 (150 mM), VH032 (250 mM or 1 mM) or 1 mMof CM11.

FIG. 11. Compound activity is CRL2VHL and proteasome dependent. HeLacells treated with CM11 in the absence or presence of proteasomeinhibitor MG132, MLN4924, VHL inhibitor VH032 or PHD2 inhibitor IOX4.

FIG. 12. Biophysical studies of Homo-PROTACs binding to VHL. (a)Superposition of the integrated ITC heat curves of CM11 CMP99 or CMP98titrations against VCB. (b) SEC assay of complex formation afterincubation of CM11, CMP98, CMP99, VH032 or DMSO with VCB. (c) AlphaLISA:intensity values titrating CM09, CM10, CM11 and CMP98 against VCB. Eachpoint is mean (±SEM) intensity of four technical replicates.

FIG. 13: Proposed model for the mechanism of action of Homo-PROTAC CM11.

FIG. 14: HeLa or U2OS cells stably expressing HRE-luciferase reporterplasmid were treated with the indicated compounds at the indicatedconcentrations for the indicated time.

FIG. 15: Dose-response curve of CA9 mRNA expression in HeLa (16 h)

FIG. 16: Hela cells were treated with increasing concentration ofindicated compound for 4 h or 24 h.

FIG. 17: Concentration dependency experiment in U2OS (10 htreatment)(left) and Time course experiments of lysate from U2OS(right).

FIG. 18: Time-course immunoblots of lysates from HeLa cells subjected to0.1% DMSO, CoCl2 (100 μM), IOX2 (150 μM), VH032 (250 μM or 1 μM) or 1 μMof indicated compounds.

FIG. 19: Integrated ITC heat curves of CM09 (a), CM10 (b), and CM11 (c)against VCB.

FIG. 20: Superposition of the integrated ITC heat curves of CM11, CM09,or CM10 titrations against VCB.

FIG. 21: SEC assay of complex formation after incubation of CM11, CM09,CM10 or DMSO (black) with VCB.

FIG. 22: Immunomodulatory drugs targeting cereblon. (a) Chemicalstructures. (b) Crystal structure of pomalidomide bound to CRBN (PDBcode 4Cl3)⁵

FIG. 23: Structure of Hetero-PROTACs designed to recruit CRL4^(CRBN) atone end and CRL2^(VHL) at the other end.

FIG. 24: Synthesis of intermediates 29 and 45.

FIG. 25: Synthesis of 52 (CMP85) and 51 (CMP86)

FIG. 26: Side product 53 of cyclization reaction.

FIG. 27: Chemical structures of CM09, CM10, CM11,

FIG. 28: HeLa, Hek293 and U2OS cells were treated with 1 μM of CM09,CM10, CM11, DAT265, CMP85 or CMP86, 0.1% DMSO, CoCl₂ (100 μM), IOX2 (50μM), IOX4 (50 μM)

FIG. 29: Integrated ITC heat curve for CMP106 against VCB.

FIG. 30: Integrated ITC heat curve for CMP108 against VCB.

FIG. 31 Integrated ITC heat curve for CMP112 against VCB.

FIG. 32: Integrated ITC heat curve for CMP113 against VCB.

FIG. 33: Superposition of the integrated ITC heat curves for CM09, CM10,CM11, CMP112, CMP113, CMP106, CMP98 and CMP99 against VCB

DETAILED DESCRIPTION

While the making and using of various embodiments of the presentinvention are discussed in detail below, it should be appreciated thatthe present invention provides many applicable inventive concepts thatcan be embodied in a wide variety of specific contexts. The specificembodiments discussed herein are merely illustrative of specific ways tomake and use the invention and do not delimit the scope of theinvention.

To facilitate the understanding of this invention, a number of terms aredefined below. Terms defined herein have meanings as commonly understoodby a person of ordinary skill in the areas relevant to the presentinvention. Terms such as “a”, “an” and “the” are not intended to referto only a singular entity, but include the general class of which aspecific example may be used for illustration. The terminology herein isused to describe specific embodiments of the invention, but their usagedoes not delimit the invention, except as outlined in the claims.

Biology

Human cell lines HeLa, U2OS and HEK 293, purchased from ATCC, werepropagated in DMEM supplemented with 10% fetal bovine serum (FBS),L-glutamine, 100 μg ml⁻¹ of penicillin/streptomycin at 37° C. and 5%CO₂. Cells were maintained for no more than 30 passages. All cell lineswere routinely tested for mycoplasma contamination using MycoAlert kitfrom Lonza.

Small Interfering RNA.

For siRNA inhibition studies, 3×10⁵ cells were seeded into each well ofa 6-well plate in order to achieve 70% of confluence on the day oftransfection. siRNA (SMARTpool: ON-TARGETplus VHL siRNAL-003936-00-0005) was prepared as a 20 μM solution in RNase-free 1×siRNA buffer. Negative control siRNA (siRNA from Life Technologies, cat.#4390843) was used as negative control. On the day of transfection, oldmedium was replaced with fresh one. siRNA solution (5 μL) of both VHLtargeting siRNA and negative control were added to 250 μL of Opti-mem in1.5 mL tube. This solution was prepared in duplicate. The content ineach tube was mixed by pipetting. Lipofectamine RNAiMax (5 μL) was addedto 250 μL of

Opti-mem in another 1.5 mL tube. The solution was prepared in duplicate.The content in each tube was mixed by pipetting. The solution from step2 was added to the tube in step 3. The solution was mixed by briefvortex ad incubated at r.t. for 20 min. The tubes were centrifugedbriefly. The whole volume of transfection mix was added to the 6-wellplate. Plate was swirled gently back and forth to mix the content.Plates were incubated at 37° C. and 5% CO₂ for 48 h before harvesting.

Single Point Treatment.

For single time point treatment experiments, cells were transferred in6-well plates with 5×10⁵ cells per well in 2 ml media in order toachieve 80% confluence the following day. Stock concentrations ofcompounds were prepared by solubilizing the powder in 100% v/v DMSO tothe final desired stock concentration.

On the day of treatment, all compound samples were prepared as 100-foldconcentrated compound solution using DMEM just before treatment. Theexperiment samples (20 μL) were added to the 6 well plate containing 2ml of media. The final DMSO concentration was 0.1% v/v. Cells wereincubated at 37° C. and 5% CO₂ for the desired time before harvesting.

Time Course Experiments.

For time dependent treatment, cells were transferred in 6-well plateswith 3×10⁵ cells per well in 2 ml media. Samples were prepared asdetailed above or the single time point experiments. Treatment wasconducted at given time points prior to harvest.

ML4924 and MG132 Treatment.

Cells were transferred in 6-well plates with 5×10⁵ cells per well in 2ml media in order to achieve 80% confluence the day after. At t=0,MLN4924 was added into the desired wells at 3 μM final concentration and0.1% v/v of DMSO. DMSO (0.1% v/v final conc.) was added to the remainingwells in order to match identical conc. of vehicle in all wells. At t=3h, MG 132 was added into the desired wells at 50 μM final conc. and 0.1%v/v of DMSO. DMSO (0.1% v/v final conc.) was added to the remainingwells in order to achieve the same conc. of vehicle in all the wells. Att=3.5 h, the desired wells were treated with 1 μM of CM11 in 0.1% v/vDMSO final concentration. DMSO (0.1% v/v final conc.) was added to theremaining wells in order to obtain the same conc. of vehicle in all thewells. The total final concentration of DMSO was therefore 0.3% v/v.Plates were incubated for 4 h at 37° C. and 5% CO₂ before harvesting.

Competition Experiments with VH032.

Cells were transferred in 6-well plates with 5×10⁵ cells per well in 2ml media in order to achieve 80% confluence the day after. On the day ofexperiment, cells were treated with VH032 at the final conc. of 150 μMfor 30 min prior to treatment with CM11 at 1 μM final concentration for4 h. Plates were incubated for the desired time at 37° C. and 5% CO₂before harvesting.

Co-Treatment with IOX4 and CM11 to Investigate Upstream EffectExperiment.

For this experiments, cells were transferred in 6-well plates with 5×10⁵cells per well in 2 ml media in order to achieve 80% confluence the dayafter. On the day of experiment, cells were treated with IOX4 at thefinal concentration of 50 μM for 30 min prior to treatment with CM11 at1 μM final concentration for 4 h. Plates were incubated for the desiredtime at 37° C. and 5% CO₂ before harvesting.

Immunoblotting.

Cells were lysed in lysis buffer (20 mM Tris pH 8, 150 mM NaCl, 1%Triton×100) and a protease inhibitor cocktail (Roche) per 10 ml buffer.For protein extracts, the dishes were placed on ice. The media wasaspirated and the tissue layer washed twice with ice-cold phosphatebuffer saline (PBS). Lysis buffer (120 pl) was added and the cellsdetached from the surface with a cell scraper. After removal of theinsoluble fraction by centrifugation, the protein concentration of thesupernatant was determined by Pierce™ Coomassie (Bradford) Protein AssayKit. Protein extracts were fractionated by SDS-PAGE on 4-12%Tris-Acetate NuPage® Novex® (Life Technologies) polyacrylamide gels andtransferred to a nitrocellulose membrane using wet transfer. Themembrane was then blocked with 5% w/v Bovine serum albumin (BSA) inTris-buffered saline (TBS) with 0.1% w/v Tween-20. For detectingproteins the following primary antibodies in the given concentrationswere used: anti-β-Actin (Cell Signaling Technology, 4970S, 13E5) 1:2000,anti-VHL (Cell Signaling Technology, #68547) 1:1000, anti-Hif-1α (BDBiosciences, 610959, clone 54) 1:1000, anti-hydroxy-HIF-1α (Hyp564)(Cell Signaling Technology; #3434) 1:1000, anti-PHD2 (BethylLaboratories; A300-322A) 1:1000, anti-PHD3 (Bethyl Laboratories;A300-327A) 1:1000, anti-CRBN (Proteintech; 11435-1-AP) 1:1000.

Following incubation with a horseradish peroxidase-conjugated secondaryantibody (Cell Signaling Technology), the signal was developed usingenhanced chemiluminescence (ECL) Western Blotting Detection Kit(Amersham) on Amersham Hyperfilm ECL film (Amersham).

Band quantification was performed using ImageJ software and reported asrelative amount as ratio of the each protein band relative to the lane'sloading control. The values obtained were then normalized to 0.1% DMSOvehicle control.

Luciferase Assay.

It was performed essentially as described by Frost et al.³⁴ Briefly,cells (HeLa and U2OS) stably expressing an HRE-luciferase reporter weretreated for the indicated times with compounds. Cells were harvested inpassive lysis buffer (Promega) and subjected to three freeze-thawcycles. The soluble lysate fraction was used for assays, performedaccording to the manufacturer's instructions (Promega) using a BertholdLumat LB 9507 Luminometer. Results were normalized for proteinconcentration, and reported as mean±s.e.m. from three biologicalreplicates.

Quantitative Real-Time PCR.

It was performed essentially as described by Frost et al.³⁴ Briefly, RNAwas extracted from HeLa cell lysates using the RNeasy Mini Kit (Qiagen)and reverse transcribed using the iScript cDNA Synthesis kit (Bio-Rad).Real-time PCR was performed using PerfeCTa SYBR Green FastMix (QuantaBiosciences) in C1000 Touch Thermal Cycler (Bio-Rad). mRNA levels werecalculated based on averaged Ct values from two technical replicates,normalized to mRNA levels of β-actin, and reported as mean±s.e.m. fromthree biological replicates.

Biophysical Assays

Isothermal Titration Calorimetry (ITC).

Titrations were performed on an ITC200 micro-calorimeter (GEHealthcare). PROTACs (CM11, CMP98 or CMP99) were diluted from a 100 mMDMSO stock solution to 150 μM in a buffer containing 20 mM Bis-trispropane, 150 mM NaCl, 1 mM tris(2-carboxyethyl)phosphine (TCEP), pH 7.4.The final DMSO concentration was 0.15% v/v. VBC protein experiments werecarried out in a buffer containing 20 mM Bis-tris propane, 150 mM NaCl,1 mM TCEP, 0.15% v/v DMSO, pH 7.4. The titrations consisted of 19injections of 2 μL compounds solution (150 μM, in the syringe) at a rateof 2 s/μL at 120 s time intervals into the VCB protein solution (20 μM,in the cell). An initial injection of compound solution (0.4 μL) wasmade and discarded during data analysis. All experiments were performedat 25° C., whilst stirring the syringe at 600 rpm. The data were fittedto a single binding site model to obtain the stoichiometry n, thedissociation constant K_(d) and the enthalpy of binding ΔH using theMicrocal LLC ITC200 Origin software provided by the manufacturer.

Size Exclusion Chromatography (SEC).

SEC experiments were carried out in a ÄKTA pure system (GE Healthcare)at room temperature. The oligomeric state of the VCB complex in solutionwas analyzed by gel filtration in a buffer containing 20 mM Bis-Tris (pH7), 150 mM NaCl and 1 mM 1,4-dithiothreitol (DTT) using a Superdex 200Increase 10/300 GL column (GE Healthcare) calibrated with globularproteins of known molecular weight (GE Healthcare, 28-4038-41/42). VBCprotein (50 μM) was incubated with CM11 (30 μM), CMP98 (30 μM), CMP99(30 μ£M), VH032 (30 μM) or DMSO (0.5%) for 20 min at room temperatureprior to injection. Sample volume for each injection was 200 μL, and theflow rate was 0.5 mL/min. Peak elution was monitored using ultravioletabsorbance at 280 nm.

Biotinylation of VCB.

The VCB complex was mixed with EZ-link NHS-PEG₄-biotin (ThermoScientific) in a 1:1 molar ratio and incubated at room temperature for 1h. The reaction was quenched using 1 M Tris-HCl, pH 7.5, and unreactedNHS-biotin was removed with a PD-10 MiniTrap desalting column (GEHealthcare) equilibrated with 20 mM HEPES, pH 7.5, 150 mM NaCl and 1 mMDTT.

AlphaLISA Assay.

All assays were performed at room temperature in 384-well plates with afinal assay volume of 25 μL per well; plates were sealed withtransparent film between addition of reagents. All reagents wereprepared as 5× stocks diluted in 50 mM HEPES, pH 7.5, 100 mM NaCl, 0.1%(w/v) bovine serum albumin and 0.02% (w/v)3-[(cholamidopropyl)dimethylammonio]-1-propanesulfonate (CHAPS).Biotinylated VCB (20 nM final) and His₆-VCB (20 nM final) were incubatedwith a range of Homo-PROTAC concentrations (0.5 to 200 nM; three-in-fiveserial dilution) for 1 h. Anti-His acceptor beads (PerkinElmer, 10 μg/mLfinal) were added and plates were incubated for another hour.Streptavidin-coated donor beads (PerkinElmer, 10 μg/mL final) were addedand plates were incubated for a final 1 h. Plates were read on aPHERAstar FS (BMG Labtech) using an optic module with an excitationwavelength of 680 nm and emission wavelength of 615 nm. Intensity valueswere plotted against PROTAC concentration on a logo scale.

Rational Design

Design of VHL Homo-PROTACs began with careful consideration of theposition of derivatization on two potent VHL ligands recentlycharacterized by our group, VH032 and VH298 (FIG. 1b ).^(2,3) To retainthe strong binding affinity that characterizes the ligand, co-crystalstructures were analyzed to identify solvent exposed regions from wherethe ligands could be derivatized without perturbing their binding modes(FIG. 1a ). This analysis and consideration of previous VHL-targetingPROTACs pointed to the methyl group of the left-hand side (LHS) terminalacetyl group of VH032 as a suitable point of connection for alinker.^(12,13) A second solvent-exposed position available forderivatization was the phenyl group on the right-hand side (RHS), aspreviously employed with PROTACs targeting the Halotag.³⁵ To investigatethe impact of derivatization, we designed three classes of Homo-PROTACS:a) symmetric via the LHS acetyl group of each ligand (FIG. 2a ); b)symmetric via the RHS phenyl group (FIG. 2b ); and c) asymmetric via theacetyl group in one warhead and the phenyl in the other (FIG. 2c ). Inthe cases b and c, at the underivatized terminal LHS we decided toretain either an acetyl (as in VH032) or a cyano-cyclopropyl moiety (asin VH298), a modification that led to increased binding affinities, cellpermeability and cellular activities in the context of the VHL inhibitoralone.³ To evaluate the potential impact of linker length, linkerscomprised of polyethylene glycol chains with either three, four or fiveethylene glycol units were chosen to connect the two VHL ligands.

It is known that the trans epimer of Hyp is an absolute requirement forVHL binding, and that the corresponding cis epimer abrogates binding toVHL, both within the context of a native HIF substrate peptide,³⁶ andVHL ligands.^(3,13) We therefore designed two different PROTACs based onthe structure of the first series (FIG. 2a ), with the aim to use themas controls: a cis-cis epimer, expected to be completely inactive, and acis-trans epimer compound, expected to retain binding to a single VHLmolecule in a 1:1 fashion, thus potentially acting as inhibitor but notas degrader.

Synthesis.

For the synthesis of the first class of Homo-PROTACs (FIG. 2a ),symmetric PEG linkers 4, 5 and 6 bearing free carbon/late groups ateither ends were obtained by reaction of tert-butyl bromoacetate withtri-, tetra- and penta-ethylene glycol in the presence of NaH in dioxaneand followed, after purification, by treatment with 50% TFA in DCM (FIG.3). The final compounds CM9, CM10 and CM11 were obtained by amidecoupling of the VHL ligand 7 (prepared as previously described)³⁸ withlinkers 4, 5 and 6, in a 2:1 ratio, respectively, in the presence ofHATU as the coupling agent and DIPEA as the base (FIG. 3). For thesynthesis of the symmetric cis-cis compound CMP98, compound 8 (ref. 38)was coupled with linker 6 to afford the desired product (FIG. 3).

For the preparation of the asymmetric cis-trans compound CMP99, asynthetic route toward the synthesis of the monoprotected di-carbon/latelinker was established. Pentaethylene glycol was the linker of choicebecause of ease of purification compared to longer PEGs, and at the sametime yielding a control compound of average linker length (PEG-4 in thiscase). Pentaethylene glycol was converted into monobenzyl ether 9 in 71%yield, which was reacted with tert-butyl bromoacetic acid under biphasicconditions (DCM/37% aq. NaOH and stoichiometric tetrabutyl ammoniumbromide). After deprotection of the benzyl group by catalytichydrogenation, formation of the carboxylic acid moiety was achieved byoxidation with TEMPO and bis-acetoxy iodobenzene (BAIB), deliveringcompound 11 in 65% yield (FIG. 4). Compound 7 was then coupled withlinker 11 using the condition described above, affording compound 12.Deprotection of the tert-butyl group using TFA and subsequently couplingwith 8 afforded CMP99 in 66% yield (FIG. 4).

For the synthesis of the second class of symmetric Homo-PROTACs (FIG. 2b), it was decided to utilize compounds 17 and 18 as VHL warheads. Commonprecursor 16 was synthesized following a previously reportedprocedure,³⁵ with minor modification that led to yield and purityimprovements (FIG. 5). Indeed, we observed that the use of HATU incombination with HOAT for the coupling steps of both Boc-L-Hyp andBoc-tert-leucine led to the formation of only the desired products,avoiding the formation of a bis-acylate secondary product,⁵⁴ insteadprominent when HATU was used alone. Compound 17 or 18 were obtained bytreatment of compound 16 with 1-cyanocyclopropanecarboxylic acid inpresence of HATU, HOAT and DIPEA or acetylimidazole and TEA (FIG. 5).Synthesis of 17 was also performed using acetic anhydride, but duringthis reaction it was observed the formation of a secondary productdi-acetylated, not only at the desired position but also at the hydroxylgroup of the phenyl ring, which could however be separated.

The PEG linkers for this class of compound were designed to contain amethanesulfonate group at either end, which could be coupled in a singlestep with the phenol of the VHL ligand. Linker 19 was prepared bymesylation of pentaethylene glycol and reacted with either compounds 17or 18 in a 1:2 ratio in the presence of K₂CO₃ to afford CMP106 andCMP108, respectively, in good yield (FIG. 6).

For the synthesis of asymmetric Homo-PROTACs, PEG 10 was converted in tothe mesylated derivative 20 and reacted with 17 or 18 to obtain 21 and22, respectively in good yield (FIG. 7). Final compounds CMP112 andCMP113 were obtained in good yield upon deprotection of the tert-butylgroup and amide coupling with compound 7 (FIG. 7).

Biological Evaluation.

We next tested all our Homo-PROTACs in HeLa cells, and monitored proteinlevels by Western blots after 10 h of compound treatment at 1 μMconcentration (FIG. 8a ). We observed striking effectiveness of CM09,CM10 and CM11 in inducing VHL depletion in cells (FIG. 8a ), and aremarkably selective degradation for the band corresponding to the longisoform of VHL, preferentially over the short isoform. The VHL geneincludes three exons and it encodes two major isoforms of VHL: a 213amino-acid long, 30 kDa form (pVHL30) and a 160 amino-acid long, 19 kDaform (pVHL19). pVHL19 lacks a 53 amino-acid long amino-terminal domainor N-terminal tail (pVHL-N), which is instead present in pVHL30.Although both isoforms are expressed in human cells, pVHL19 is the moreprominent form in human tissues.⁵⁶ The most active compounds aresymmetrically linked from the terminal LHS acetyl group of VH032.Linkage at different positions proved ineffective, suggesting a criticalrole played by the linking pattern on the VHL ligands. Control compoundsCMP98 and CMP99 were unable to induce degradation of VHL (FIG. 8a ),demonstrating that Homo-PROTAC activity is dependent on productivebivalent recruitment of VHL by the trans epimer. The length of thelinker also seemed to affect cellular potency. Indeed, a decrease ineffectiveness was observed at shorter linker lengths, with CM10 and CM11being the most active compounds achieving total knockdown of pVHL30,followed by CM09 depleting 82% of the target protein. Interestingly,some degradation of the short iso-form pVHL19 was also observed, albeitlow (around 10% depletion). Levels of Cullin2, the central subunit ofthe CRL2-VHL complex,⁵⁷ were also reduced upon treatment with CM10 andCM11 by up to 22% (FIG. 8a ).

Treatments with CM10 and CM11 also showed detectable albeit low increasein protein levels of the hydroxylated form of HIF-1α (Hdy-HIF-1α, FIG.8a ). As the parent inhibitor VH032 is completely ineffective at thesame concentration of 1 μM (see ref. ³ and vide infra, FIG. 8), thiseffect cannot be due to VHL inhibition and is therefore thought to bethe result of compound-induced protein degradation. Levels of HIF-1αwere, however, significantly lower than observed with the parentinhibitors VH032 when used at concentrations >100 μM (FIG. 8a , see alsoref. ³). VHL knockdown by siRNA experiments in three different celllines was consistent with CM11-induced knockdown, and also insufficientto induce significant HIF stabilization (FIG. 8b ). The siRNA resultalso confirmed that the bands observed to decrease in intensity withcompound treatment indeed correspond to VHL.

To assess whether selective pVHL19 knockdown by Homo-PROTACs couldinduce HIF transcriptional activity, we first used a luciferase reporterassay.³⁷ Hypoxia response element (HRE)-luciferase reporter HeLa-HRE andU2OS-HRE cells were treated with different concentrations of CM11 and atdifferent times, and no increase in HIF-dependent luciferase activitywas detected relative to DMSO control treatment (FIG. 14). These resultswere confirmed in a qRT-PCR assay, where no upregulation of mRNA levelsof the known HIF-target genes CA9 was detected (FIG. 15). Together thedata suggests that the un-degraded pVHL19 is sufficient to efficientlymaintain low levels of HIF-1α, and that complete knockdown of all VHLisoforms is required to achieve effective HIF stabilization in cells, asobserved in vh^(−/−) cells such as VHL-deficient renal carcinoma cells.

We next turned our attention to further characterizing the mode ofaction of the protein degradation induced by the active Homo-PROTACsCM09-11. To interrogate their relative cellular potency, dose-dependenttreatments were performed at two different time points, 4 and 24 h priorto harvesting. All compounds confirmed preferential degradation ofpVHL30 in a concentration-dependent manner, relative to thecorresponding DMSO control (see FIG. 9 for CM11, and FIG. 16 for CM09and CM10).

CM11 proved the most potent Homo-PROTAC, inducing complete depletion ofpVHL30 after 4 h already at 10 nM (DC₉₉=10 nM, FIG. 9). Selective pVHL30knockdown was retained after 24 h, with half-degrading concentration(DC₅₀) between 10 and 100 nM. The effective degrading concentrations ofCM11 are >3 orders of magnitude lower than the inhibitory concentrationsof the constitutive ligand VH032 alone, which is only active in cells at˜100 μM, underscoring the profound difference in cellular efficacybetween the two mode of actions. Cellular levels of Cullin2 decreased byup to 73% upon treatment with CM11 (FIG. 9). As previously observed,selective pVHL30 knockdown by Homo-PROTACs resulted in only minorincrease in levels of HIF-1α, relative to hypoxia-inducing controlsCoCl₂, PHD inhibitor IOX2, and VH032 (FIG. 9). However, when tested athigh micromolar concentrations, Homo-PROTACs acted preferentially as VHLinhibitors over VHL degraders, consistent with the so-called“hook-effect” whereby formation of binary 1:1 complexes competes withand eventually supersedes the formation of the productive catalytic 2:1complex.⁵⁹ Stabilization of Hdy-HIF-1α upon treatment with all threecompounds at 100 μM was indeed comparable with the effect obtained withVH032 alone (FIG. 9 for CM11, and FIG. 16 for CM09 and CM10). To confirmthe cellular activities of Homo-PROTACs in a different cell line, asimilar experiment was performed treating U2OS cells for 10 h with CM09,CM10 and CM11 using the same range of concentrations (1 nM-100 μM). Aconsistent profile of cellular activity was observed, confirming thatthe effects observed are independent from cell type (FIG. 17).

We next interrogated the time-dependent activity of Homo-PROTACs.Progressive removal of VHL protein over time was observed, confirmingselective depletion of pVHL30 over the short isoform (FIG. 10 for CM11and FIG. 18 for CM09 and CM10). In particular, CM11 was confirmed to bethe most effective compound, decreasing pVHL30 level by more than 70%already after 2 h of treatment, and essentially to completion after 8 h.The depletion effect was retained up to 12 h; however, interestingly,pVHL30 levels up to 11% were detected after 24-36 h treatment, to thendecrease again after 48 h. Incomplete degradation of pVHL was observedupon treatment with CM09, even in the longer time points (FIG. 18). Asbefore, minor stabilization of Hdy-HIF-1α over time was observed for allthree compounds, most pronouncedly up-on treatment with CM11. Theresults obtained treating U2OS cells were consistent with what observedin the previous experiment. However, in this cell line all the threecompounds were able to induce complete degradation of pVHL30 over time(FIG. 17). We hypothesize that this could be due to the lower expressionlevel of VHL in U2OS, leading to faster cellular depletion compared tocell lines where VHL level is higher. CM09 and CM10 achieved completedegradation of the target protein after 2 h of treatment. CM11 confirmedto be the most potent compound also in this cell line, achievingcomplete degradation of pVHL30 already after 1 h. Interestingly CM09lost its cellular efficacy after 36 h. In contrast, both CM10 and CM11retained their efficacy even at these longer time points (FIG. 17).

TABLE 1 Summary of thermodynamic binding parameters of Homo-PROTACs andcomparison with VHL inhibitor VH032 (from 19) measured by ITC, againstboth short and long VHL isoforms. −TΔS Protein Compound n Kd (nM) α ΔG(kcal/mol) ΔH (kcal/mol) (kcal/mol) pVHL19 VH032 (ref. ²) 1.030 ± 0.001188 ± 6  — −9.17 ± 0.02 −5.53 ± 0.01 −3.65 ± 0.02 CM11  0.6 ± 0.01 11 ±2 18 −10.9 ± 0.1  −12.3 ± 0.7   1.4 ± 0.8 CMP99 0.964 ± 0.005 146 ± 2  —−9.33 ± 0.06 −6.23 ± 0.05 −3.1 ± 0.7 CM09 0.98 ± 0.09  41 ± 15 4 −10.3 ±0.2  −6.9 ± 0.3 −3.5 ± 0.5 CM10 0.73 ± 0.01 32 ± 5 6 −10.2 ± 0.1  −9.4 ±0.1 −0.8 ± 0.2 CMP106 0.535 ± 0.004 111 ± 8  1.7 −9.5 −12.6 ± 0.1  3.1CMP112 0.498 ± 0.006 235 ± 22 0.8 −9.1 −14.8 ± 0.2  5.8 CMP113 0.934 ±0.005 117 ± 25 1.7 −9.5 −6.4 ± 0.2 −3.1 pVHL30 CM11 0.866 ± 0.003 25 ± 34 −10.4 ± 0.1  −11.3 ± 0.1  −0.9 ± 0.1 CMP99 1.050 ± 0.004 106 ± 10 —−9.51 ± 0.05 −5.19 ± 0.03 −4.3 ± 0.1

To gain mechanistic insights in the cellular activity of Homo-PROTACs,the dependency on CRL2-VHL and proteasome activities was examined. Thereliance of the Homo-PROTAC-induced protein degradation on CRL2-VHL wasassessed by inhibiting neddylation of Cullin2 using the NAE1 inhibitorMLN4924, which blocks the activity of CRLs, including CRL2-VHL.Proteasome-dependency was interrogated by treating cells with theproteasome inhibitor MG132. To limit the known cytotoxicity of MLN4924and MG132, HeLa cells were pre-treated with MLN4924 for 3 h followed byMG132 for 30 min before adding CM11 to the media, and cells wereincubated for further 4 h before harvesting. Single treatments withDMSO, MLN4924, MG132 and CM11 and combinations thereof were performed todisentangle the individual and combined effects of compound treatments.Degradation of pVHL30 induced by CM11 was completely abrogated whencells were pre-treated with MG132, establishing the expectedproteasome-dependence of the chemical intervention (FIG. 11).CM11-induced degradation was also prevented by pre-treatment withMLN4924, confirming the dependency on the activity of CRL2VHL (FIG. 11).The same effect was observed when cells where co-treated with MLN4924and MG132 prior to CM11 (FIG. 11). Immunoblots of Cullin2 levelsconfirmed the effective blockade of Cul2 neddylation by MLN4924 (FIG.11). To assess if CM11 de-grading activity was dependent on VHL binding,a competition experiment was performed using the VHL inhibitor VH032.20HeLa cells were pre-treated with VH032 at 150 μM for 30 min beforeadding CM11 into the media. The plates were incubated for further 4 hbefore harvesting. As expected, VH032 blocked pVHL degradation (FIG. 11)consistent with the hypothesis that VHL induces degradation of itself.In contrast, pre-treatment with IOX4, a PHD2 inhibitor, did not impactthe cellular activity of CM11 (FIG. 11).

Biophysical Evaluation

Key to the catalytic mode of action of PROTACs is the formation of aternary complex.^(13,15) In the case of our Homo-PROTAC compounds, VHLacts as both the E3 ligase and the substrate. Therefore, we next soughtto monitor and biophysically characterize the ternary complexVHL:Homo-PROTAC:VHL that is thought to underlie cellular activity. Toassess the formation of this ternary complex species in solution,isothermal titration calorimetry (ITC), size exclusion chromatography(SEC) and AlphaLISA proximity assays were performed (FIG. 12). In ITCtitration of CM11 against the VCB complex (VHL with Elongin B andElongin C) the stoichiometry of binding (n value) was found to be 0.6,instead of 1 with VH032 (FIG. 12a , Table 1). This result is consistentwith CM11 binding to VHL in a 1:2 molar ratio, in contrast to VH032 thatbinds to VHL in a 1:1 ratio.¹⁹ Notably, the K_(d) value measured forCM11 was 11 nM (Table 1). Closer examination of the titration curverevealed that only one point features during the inflection of thecurve. Indeed, because the protein concentration used in the experimentwas 20 μM, the c value (defined as [P]_(tot)/K_(d)) calculated for thisexperiment is 2500, which is well above the upper limit of c (around500-1000) that is a prerequisite for precise measurement of bindingaffinity. Consequently, this analysis suggests that we may beunderestimating the binding affinity of CM11, i.e. we can conclude thatK_(d) is ≤118 nM. This corresponds to an avidity (also known ascooperativity α) of >18-fold when compared to VH032. Such large avidityof homobivalent molecules has been observed previously with othersystems, for example the BET inhibitor MT1. The binding interactionbetween CM11 and VHL was driven by a large apparent binding enthalpy(ΔH=−12.3 kcal mol⁻¹), whereas the entropic term was slightlyunfavourable (−TΔS=1.4 kcal mol⁻¹). This observation underlines how thethermodynamic signature of CM11 is also very different when comparedwith that of VH032, in which case the binding ΔH was around half thatobserved with CM11, and both the enthalpic and entropic term contributedfavourably to the ΔG of binding (Table 1). By contrast, thethermodynamic values obtained for CMP99 binding were entirely consistentwith the ones of VH032 (Table 1). Specifically, CMP99 bound to VHL in a1:1 ratio, as expected due to the presence of the cis-Hyp in one of thetwo moieties, and it exhibited comparable ΔH and K_(d) values to VH032.As expected, binding was not detected with CMP98, the inactive cis-cisepimer. Superposition of integrated heat curves of CM11, CMP98 and CMP99is shown in FIG. 12b and visually highlights the different behaviours ofthe three compounds. CM10 showed similar thermodynamic bindingparameters relative to CM11, with n value equal to 0.7 and a low K_(d)of 32 nM. A stoichiometry close to 1 was instead found for CM09,suggesting that at the end of the titration this system was primarilypopulated by 1:1 complexes (FIGS. 19 and 20), consistent with its loweravidity (Table 1). ITC experiments were also conducted with compoundsCMP106, CMP108, CMP112 and CMP113, and the results are discussed below.

SEC experiments showed that VCB migrates more quickly in the presence ofthe active compound CM11 (2:1 protein:ligand ratio), relative to thevehicle control (FIG. 12b ). The shifted peak eluted at a volumecorresponding to a species of ˜90 kDa molecular weight, based on acalibration run with globular proteins of known molecular weight (seeMethods below), suggesting the peak corresponds to the ternary complex(VCB)₂:CM11. In contrast, there is no shift in VCB following incubationwith inactive CMP98, CMP99 or ligand VH032. Only in the samplecontaining CMP99 a small peak eluted at 13.5 ml (FIG. 12b ). It ispossible that such peak could be due to the formation of a lowlypopulated ternary complex. It is interesting that Schofield andcolleagues observed weak binding of a cis-hydroxyprolyl containingHIF-1α peptide to VHL.³⁶ This weak binding, potentially enhanced by highavidity in the ternary complex, could be responsible for the smalldecrease of VHL levels observed during biological tests in cells (FIG.8a ). CM10 and CM09 showed formation of a ternary complex eluting atidentical retention volume when compared to CM11 (FIG. 21). No evidenceof aggregation was seen with any of the compounds evaluated, as allobserved peaks eluted well after the void volume.

Lastly, we employed an AlphaLISA proximity assay to compare ternarycomplex formation by CM09, CM10 and CM11. The assay showed the highestintensity signal for CM11, whereas negligible levels of complexformation were detected for CM09 and CM10 (FIG. 12c ). Since SECdetected ternary species with all three compounds, the minimal intensitydetected in the AlphaLISA likely reflects the inability of CM09 and CM10to yield a significant ternary population at the low concentrationsrequired for the assay. These results indicate that CM11 is the mosteffective Homo-PROTAC at driving ternary complex formation, consistentwith CM11 exhibiting the highest avidity and full 2:1 stoichiometry inITC. Together, the biophysical data supports CM11 as the mostcooperative Homo-PROTAC in vitro, and provide a molecular rationaleexplaining its potent VHL-degrading activity inside cells.

Discussion

In some embodiments, Homo-PROTACs are described, a small-moleculeapproach to effectively dimerize an E3 ubiquitin ligase to induce itsown self-destruction. Using potent ligands for the E3 ligase VHL, aseries of symmetric homo-bivalent molecules that induce remarkablyrapid, profound and selective degradation of the long isoform of pVHL atnanomolar concentrations were developed. Compound-induced degradationwas exquisitely dependent on the linkage pattern on the VHL ligand. Themost active Homo-PROTAC, CM11, induces complete depletion of pVHL30after 4 h already at 10 nM. Potent and selective degradation of pVHL30was long lasting, with half-degrading concentration (DC₅₀) ofapproximately 100 nM, a remarkable increase in cellular activityof >1000-fold compared to the parent inhibitor VH032. Mechanistically,it has been shown that CM11 activity is strictly dependent on proteasomeactivity, Cul2 neddylation, and on VHL binding, and specifically on theformation of an avid 2:1 complex with VHL. The data therefore supports amodel in which a highly cooperative ternary complex VHL-CM11-VHLfunctions as the key species responsible for the induced degradation ofVHL itself (FIG. 13), which will warrant future structural studies.Interestingly, CM11 also led to a decrease in cellular levels ofCullin2, which we hypothesize to be the result of direct ubiquitinationof Cullin2 as part of the CRL2vHL complex. To our knowledge, this isfirst demonstration that a PROTAC can induce the degradation of aprotein forming part of the same complex with the protein targeteddirectly.

The preferential induced degradation of pVHL30 over the short VHLisoform was unexpected and is an intriguing result of this work. Thisobservation adds to recent evidence from us and others that chemicaldegraders designed from inhibitors recruiting more than a single proteinparalog or isoform can add a layer of target degradation selectivityindependently of target engagement.^(12,15,18) As the binary engagementof the VHL warhead was found to be similar between the two VHL isoforms(Table 1), the observed selectivity could be due to large differences incooperativities, which would impact on the relative population ofternary complexes.¹⁵ However, CM11 actually exhibited greater avidity invitro for the short relative to the long isoform of VHL (Table 1). Wetherefore view it as unlikely that the remarkable selectivity of VHLdegradation is due to large differences in cooperativities of ternarycomplexes. We also consider unlikely that preferential and moreefficient lysine ubiquitination could play a role, because the extraregion present in the long isoform (1-53) does not contain a singlelysine residue. On the other hand, this region is predicted asintrinsically disordered, and indeed it has been shown that proteinscontaining disordered N-terminal regions are more prone to proteasomaldegradation. It is also known that VHL is resistant to proteasomaldegradation when in complex with ElonginB and ElonginC, so the formobserved to be preferentially depleted may be free VHL i.e. unbound toElongins, or other proteasome-sensitive forms. Addressing thesequestions will be of clear importance for future investigation.

Selective degradation of pVHL30 by CM11 led to minimal stabilization ofHIF-a in cells, and as a result did not trigger HIF-dependent activityin cells. This highlights the potential benefit of using CM11 tointerrogate the biological function of specific VHL isoforms, withoutthe masking downstream effects of a hypoxic response. Not much is knownabout the individual roles of VHL isoforms. Studies have highlighted howthe 53-residue extra region of pVHL30 is not needed for tumorsuppression, and how both isoforms can have HIF-dependent tumorsuppressor functions in vivo. Other HIF-independent roles of pVHL havebeen proposed, including a role for pVHL in collagen assembly. However,the individual roles of the different isoforms in these biologicalfunctions remain elusive. Moreover, many HIF-independent roles arethought to be independent upon Hyp recognition, and thus cannot beprobed chemically using current Hyp-based VHL inhibitors. Selective andacute knockdown of pVHL30 by CM11 provides therefore a novel chemicaltool to address these questions.

In summary, we present CM11, a chemical probe for rapid and selectivepVHL30 knockdown. CM11 provides an alternative advantageous chemicaltool to conventional knockdown RNAi approaches and gene editing knockouttechnologies such as CRISPR-Cas9. Relevant information to the use ofCM11 will be made available in the newly established “Chemical ProbesPortal” (http://www.chemicalprobes.org/).³⁸ We anticipate CM11 will findwide use amongst chemical and cell biologists alike interested ininvestigating and dissecting the pleiotropic biological functions ofpVHL. More generally, we provide first proof-of-concept that bivalentmolecules can be designed to induce an E3 ligase to destroy itself. Thisstrategy could provide a powerful new approach to drugging E3 ligases inways that may not be possible with inhibitors alone.

Synthesis of PROTACs Recruiting Together CRL4^(CRBN) and CRL2^(VHL).

For the synthesis of compounds CMP85 and CMP86 (structures shown in FIG.23), the linker 26 and its analogue with two PEG units 43 weresynthesized adopting the same route used for 26 (FIG. 24). These linkerswere then coupled to compound 27, delivering compounds 28 and 44,respectively. Subsequent deprotection of the tert-butyl group affordedcompound 29, with a length of four PEG units, and 45, with two PEG unitsinstead (FIG. 24).

Compound 48 (the desired thalidomide derivative, see Figure) wassynthesized as previously published by Lu et al.¹⁷ In the first step,3-fluorophthalic acid was dehydrated with acetic anhydride to obtaincompound 46 in good yield. Reaction of compound 46 with L-glutamine andsubsequent treatment with HCl 4 M solution led to the formation ofcompound 47. Cyclization of 47 was performed at reflux in the presenceof 1,1′-carbonyldiimidazole (CDI) and DMAP. The recommended time forthis step was 5 h. After 2.5 h it was possible to observe the formationof a side product by LC-MS. For this reason, even if the reaction wasnot completed, the reaction was cooled to r.t. and the resulting solidcollected by filtration. During the purification step, performed bycolumn chromatography over silica, compound 48 was isolated in goodyield. The side product was isolated as well and analysed by NMR andidentified to be compound 53 (FIG. 26). Compound 53 is the product of anaromatic nucleophilic substitution at position 4 of the phthalicanhydride by the nitrogen lone pair of imidazole, which is itself abyproduct of the reaction between 47 and CDI.

Compound 48 was converted into compound 50 in two steps (FIG. 25), bycoupling with N-Boc-ethylenediamine and subsequent Boc deprotection inacidic conditions. Coupling of the latter with 29 or 45 affordedcompounds 52 (CMP85) and 51 (CMP86) respectively in good yield.

Biological Evaluation of the VHL-Targeting Compounds

The following section outlines the results of the biological evaluationof PROTAC compounds targeting VHL in cells.

In order to assess the activity of compounds inside cells, HeLa cellswere treated with 1 μM of Homo-PROTACs CM09, CM10 and CM11 (FIG. 27)synthesis of which are below, and the above described PROTACs recruitingCRL4^(CRBN) to target VHL, i.e. CMP85 and CMP86.

Dimethylsulfoxide (DMSO vehicle, 0.1% v/v), CoCl₂ (chemical inducer ofHIF-1α), IOX2 and IOX4 (selective inhibitor of PHD2), VH032 (selectiveVHL inhibitor) were used as controls. The samples, obtained after 10 hof treatment and cell lysis, were resolved by SDS-PAGE followed byWestern blot using the corresponding specific antibodies to probe forthe following proteins (FIG. 28):

-   -   VHL: CM09, CM10 and CM11 demonstrated complete depletion of VHL        levels, which featured as a preferential or selective        degradation of the long isoform pVHL30. However, some        degradation of the short isoform pVHL19 was also observed,        albeit only around 20%. None of the other compounds were able to        induce degradation of VHL.    -   Cullin2: To assess if treatment with the series of compounds        could have any effect on other subunits of the CLR2^(VHL),        protein levels of Cullin2 were evaluated. CM10 and CM11 showed        to affect Cullin2 levels by inducing a reduction of        approximately 20%.    -   CRBN: No detectable effect was observed on CRBN levels upon        treatment with CMP85 and CMP86.    -   HIF-1α and Hdy-HIF-1α. To evaluate if VHL degraders could induce        accumulation of HIF-1α, and specifically of its hydroxylated        form (Hdy-HIF-1α), levels of these proteins were evaluated. It        was observed during siRNA experiments that VHL knockdown does        not lead to HIF-1α depletion. Indeed, even very low levels of        VHL are capable of highly efficient catalysis on HIF-1α, leading        to subsequent effective HIF-1α degradation. As expected, VHL        depletion did not impact significantly on HIF-1α level (compare        the detected HIF-1α band with vehicle control DMSO).        Nevertheless, a slight increase of HIF-1α level was induced by        the active VHL degraders CM09, CM10 and CM11 (see HIF-1α band        with longer exposure). This effect was even more pronounced on        Hdy-HIF-1α, consistent with the stabilized HIF being in the        hydroxylated form as expected from VHL knockdown.    -   PHD2 and PHD3: to study potential hypoxic response of cells due        to treatment with the compounds, levels of PHD2 and PHD3 were        considered. No effect on the levels of these proteins was        observed at this concentration.

The same experiments were performed in other cells lines to furtherassess the consistency of the cellular effects of our compounds, asdifferent cell lines can have different expression levels of differentproteins. For example, HEK293 are known to have higher expression levelsof total VHL, which we confirmed by Western blot (FIG. 28). The sameactivity profile in decreasing preferentially pVHL30 levels by CM09-11was observed in HEK 293 (FIG. 28). No major effects were observed onlevels of the other proteins. Experiments conducted in U2OS cells showedthe same results, confirming that the effect observed upon treatmentwith CM09, CM10 and CM11 is independent from cell type and it isconsistent in all tested cell lines (FIG. 28).

ITC experiments were also conducted with compounds CMP106, CMP108,CMP112 and CMP113 (data shown in FIGS. 29-32). With the exception ofcompound CMP108 for which data could not be fitted to a binding curve,all of the other compounds exhibited very similar binding affinity asthe individual warhead ligand (cooperativity around 1), suggesting theyare much less cooperative than CM11, which is consistent with their lackof activity in cells. This conclusion is illustrated in FIG. 33, wherethe ITC titrations for compounds CM09-11, CMP112-113, CMP106 as well ascontrol compounds CMP98 and CMP99 are all superposed together in asingle Figure, highlighting the remarkable potency and cooperativity ofCM11.

Materials and Methods

All chemicals were purchased from commercial vendors and used withoutfurther purification, unless indicated otherwise. Reactions weremagnetically stirred; commercially available anhydrous solvents wereused. All reactions requiring anhydrous conditions were carried outunder argon or nitrogen atmosphere using oven-dried glassware.HPLC-grade solvents were used for all reactions. Flash columnchromatography was carried out using silica gel (Merck 60 F254 nm).Normal phase TLC was carried out on pre-coated silica plates (Kieselgel60 F254, BDH) with visualization via UV light (UV 254/365 nm) and/orbasic potassium permanganate solution or other suitable stains. Flashcolumn chromatography (FCC) was performed using a Teledyne IscoCombiflash Rf or Rf200i, prepacked columns RediSep Rf Normal PhaseDisposable Columns were used. NMR spectra were recorded on a BrukerAscend 400 or 500. Chemical shifts are reported in parts per millionreferenced to residual solvent peaks (CDCl₃=7.26 ppm). The followingabbreviations were used in reporting spectra, s (singlet), d (doublet),t (triplet), q (quartet), m (multiplet), dd (doublet of doublets). Onlymajor rotamer NMR spectra are reported. High Resolution Mass Spectra(HRMS) were recorded on a Bruker microTOF. Low resolution MS andanalytical HPLC traces were recorded on an Agilent Technologies 1200series HPLC connected to an Agilent Technologies 6130 quadrupole LC/MS,connected to an Agilent diode array detector. The column used was aWaters XBridge column (50 mm×2.1 mm, 3.5 μm particle size). The flowrate was 0.6 mL/min. Preparative HPLC was performed on a GilsonPreparative HPLC System with a Waters XBridge C18 column (100 mm×19 mm;5 μm particle size).

General method A: PEG was solubilised in dioxane anhydrous and NaH wasadded under stirring. The resulting mixture was stirred at r.t. for 3 h.The mixture was cooled down to 0° C. using ice bath and tert-butylbromoacetate was added drop by drop. The resulting mixture was stirred at r.tO/N. The precipitate was filtered off and the organic phase evaporatedto dryness. The resulting oil was taken up with ethyl acetate, washedwith water, dried over MgSO₄ and evaporated to dryness. The resultingoil was purified by column chromatography using a gradient of ethylacetate from 50% to 100% v/v in heptane.

General method B: tert-butyl esters 1, 2, 3 or 12 were dissolved in asolution of 50% v/v trifluroacetic acid in DCM. The resulting solutionwas stirred for 1 h or until complete conversion of starting material.The solvent was removed under high vacuum. The resulting carboxylic acidwas used as crude in the next step without any further purification. Toa solution of carboxylic acid in 1 ml DMF were added HATU (1 eq.) andHOBT (1 eq.) and the solution was stirred at room temperature for 5 min.Amine 6, 31 or 32 was added and the pH of the reaction mixture wasadjusted to >9 by addition of DIPEA (3 eq.). The mixture was stirred atroom temperature until no presence of the starting materials wasdetected by LC-MS. Water was added and the mixture was extracted withethyl acetate (×3). The combined organic phases were washed with brine(×2), dried over MgSO₄ and evaporated under reduced pressure to give thecorresponding crude, which was purified by HPLC using a gradient of 20%to 95% v/v acetonitrile in 0.1% aqueous solution of ammonia to yield thedesired compound.

General method C: A mixture of mesilate, compound 6, 31, 32, and K₂CO₃(41.46 mg, 0.3 mmol, 6 eq.) in DMF was stirred O/N at 70° C. Thereaction mixture was filtered off to afford the crude product, which waspurified by HPLC using a gradient of 5% to 95% v/v acetonitrile in 0.1%aqueous solution of formic acid to yield the desired compounds.

(2S,4R)-4-hydroxy-N-(2-hydroxy-4-(4-methylthiazol-5-yl)benzyl)pyrrolidine-2-carboxamidehydrochloride (15)

To a solution of trans-N-(tert-Butoxycarbonyl)-4-hydroxy-L-proline (890mg, 3.84 mmol, 1 eq.) in DMF was added HATU (1.46 g, 3.84 mmol, 1 eq.)and HAOT (522 mg, 3.84 mmol, 1 eq.) and the solution was stirred at roomtemperature for 5 min. 14 (846 mg, 3.84 mmol, 1 eq.) was added and thepH of the reaction mixture was adjusted to >9 by addition of DIPEA (3eq.) and the mixture was stirred at room temperature until no presenceof the starting materials was detected by LC-MS. Water was added and themixture was extracted with ethyl acetate (×3). The combined organicphases were washed with brine (×2), dried over MgSO₄ and evaporatedunder reduced pressure to give the corresponding crude, which waspurified by flash column chromatography using a gradient of 0 to 80% v/vacetone in heptane to yield the titled compound. Yield: 1.298 g, 3 mmol(78%). Analytical data matched those previously reported³⁵

The N-Boc-protected compound was dissolved in DCM. An equal volume of 4MHCl in dioxane was added and the reaction mixture stirred at roomtemperature for 2 h. The solvent was removed under a stream of nitrogenand dried under reduce pressure. The resulting crude was used for thenext step without any further purification (quantitative yield).Analytical data matched those previously reported³⁵

(2S,4R)-1-((S)-2-amino-3,3-dimethylbutanoyl)-4-hydroxy-N-(2-hydroxy-4-(4-methylthiazol-5-yl)benzyl)pyrrolidine-2-carboxamidehydrochloride (16)

To a solution of trans-N-(tert-Butoxycarbonyl)-4-hydroxy-L-proline (890mg, 3.84 mmol, 1 eq.) in DMF was added HATU (1.46 g, 3.84 mmol, 1 eq.)and HAOT (522 mg, 3.84 mmol, 1 eq.) and the solution was stirred at roomtemperature for 5 min. 14 (846 mg, 3.84 mmol, 1 eq.) was added and thepH of the reaction mixture was adjusted to >9 by addition of DIPEA (3eq.) and the mixture was stirred at room temperature until no presenceof the starting materials was detected by LC-MS. Water was added and themixture was extracted with ethyl acetate (×3). The combined organicphases were washed with brine (×2), dried over MgSO₄ and evaporatedunder reduced pressure to give the corresponding crude, which waspurified by flash column chromatography using a gradient of 0 to 80% v/vacetone in heptane to yield the titled compound. Yield: 1.915 g, 3.61mmol (94%). Analytical data matched those previously reported³⁵.

The N-Boc-protected compound was dissolved in DCM. An equal volume of 4M HCl in dioxane was added and the reaction mixture stirred at roomtemperature for 2 h. The solvent was removed under a stream of nitrogenand dried under reduced pressure. The resulting crude was used for thenext step without any further purification (quantitative yield).Analytical data matched those previously reported³⁵.

(2S,4R)-1-((S)-2-(1-cyanocyclopropane-1-carboxamido)-3,3-dimethylbutanoyl)-4-hydroxy-N-(2-hydroxy-4-(4-methylthiazol-5-yl)benzyl)pyrrolidine-2-carboxamide(18)

1-cyanocyclopropanecarboxylic acid (69 mg, 0.62 mmol, 1 eq.) wassolubilized in 3 ml of DMF. HATU (235 mg, 0.62 mmol, 1 eq.) and HOAT(84.4 mg, 0.62 mmol, 1 eq.) were added and the resulting mixture wasstirred at r.t. for 5 min. The amine precursor of 16 (300 mg, 0.62 mmol,1 eq.) was added and the pH was adjusted to pH>9 using DIPEA (400 mg,0.5 ml, 3.1 mmol, 5 eq.). The resulting mixture was stirred at r.t.until complete conversion of the starting material. Water was added, andthe mixture was extracted with ethyl acetate (×3). The combined organicphases were washed with brine (×1), dried over MgSO₄, and evaporated toafford the corresponding crude compound that was purified by flashcolumn chromatography using a gradient of 10% to 70% acetone in heptaneto yield the title compound as a white solid. Yield: 200 mg, 0.37 mmol(60%). HRMS (ESI) m/z: [M+H]⁺ calculated for: C₂₇H₃₃N₅O₅S: 539.22;observed: 540.3.

¹H NMR (400 MHz, CDCl3) 9.29 (1H, s), 8.65 (1H, s), 8.02 (1H, t, J=6.4Hz), 7.12 (1H, d, J=7.7 Hz), 6.99 (1H, d, J=8.0 Hz), 6.94 (1H, d, J=1.8Hz), 6.86 (1H, dd, J=1.8, 7.7 Hz), 4.72 (1H, t, J=8.0 Hz), 4.54 (1H, s),4.44-4.35 (2H, m), 4.19 (1H, dd, J=5.5, 14.6 Hz), 3.87 (1H, d, J=11.0Hz), 3.62 (1H, dd, J=3.7, 11.0 Hz), 3.50 (1H, s), 2.49 (3H, s),2.43-2.37 (1H, m), 2.13-2.06 (1H, m), 1.66-1.37 (4H, m), 0.89 (8H, s);¹³C NMR (101 MHz, CDCl₃) δ 172.8, 170.8, 165.8, 155.8, 150.5, 148.3,133.3, 131.6, 131.2, 123.9, 120.9, 119.6, 118.2, 70.1, 58.6, 58.3, 56.7,55.7, 40.0, 35.7, 26.2, 18.6, 17.9, 17.8, 17.2, 16.1, 13.8.

(2S,4R)-1-((S)-2-acetamido-3,3-dimethylbutanoyl)-4-hydroxy-N-(2-hydroxy-4-(4-methylthiazol-5-yl)benzyl)pyrrolidine-2-carboxamide(17)

The amine precursor 16 (100,7 mg, 0.240 mmol, 1 eq.) was dissolved in 1ml of DMF, acetylimidazole (31.7 mg, 0.288 mmol, 1.2 eq) and DIPEA(0.090 ml, 0.48 mmol, 2 eq.) were added to the solution. After stirringthe mixture for 48 h at room temperature, the solvent was evaporatedunder reduced pressure to give the corresponding crude, which waspurified by HPLC using a gradient of 5% to 95% v/v acetonitrile in 0.1%aqueous solution of formic acid to yield the titled compound. Yield: 91mg, 0.187 mmol (78%). ¹H NMR (400 MHz, CDCl3) 9.25 (1H, s), 8.70 (1H,s), 7.97 (1H, t, J=6.5 Hz), 7.15 (1H, d, J=7.5 Hz), 6.83-6.80 (2H, m),6.72 (1H, d, J=8.8 Hz), 4.92-4.88 (1H, m), 4.57 (1H, s), 4.52-4.42 (2H,m), 4.26-4.14 (2H, m), 3.59 (1H, dd, J=2.9, 11.1 Hz), 2.53-2.45 (4H, m),2.24-2.17 (1H, m), 1.85 (3H, s), 0.83 (9H, s); ¹³C NMR (101 MHz, CDCl₃)δ 171.8, 171.2, 155.9, 150.7, 148.1, 132.8, 131.7, 131.0, 124.2, 120.6,117.1, 70.3, 58.1, 57.7, 57.1, 39.8, 35.5, 34.8, 26.3, 22.6, 16.0. HRMS(ESI) m/z: [M+H]⁺ calculated for: C₂₄H₃₂N₄O₅S: 488.21; observed: 484.3.

di-tert-butyl 3,6,9,12-tetraoxatetradecanedioate (1)

Following general method A, from triethylene glycol (1.125 g, 1 ml, 7.49mmol, 1 eq.) in 10 ml of dioxane, NaH 60% in mineral oil (595.75 mg,14.9 mmol, 2 eq.) and tert-Butyl bromoacetate (2.905 g, 2.19 ml, 14.9mmol, 2 eq.), compound 1 was obtained as an oil after high vacuum.Yield: 538 mg, 1.42 mmol (19%).

¹H NMR (500 MHz, CDCl₃) δ 3.81 (4H, s), 3.51-3.46 (12H, m), 1.26 (18H,s). ¹³C NMR (126 MHz, CDCl₃) δ 169.1, 80.9, 70.1, 70.0, 68.5, 27.5.Analytical data matched those previously reported. ³⁹

di-tert-butyl 3,6,9,12,15-pentaoxaheptadecanedioate (2)

Following general method A, from tetrathylene glycol (1.125 g, 1 ml,5.49 mmol, 1 eq.) in 10 ml of dioxane, NaH 60% in mineral oil (463 mg,11.5 mmol, 2 eq.) and tert-Butyl bromoacetate (2.25 g, 1.7 ml, 11.5mmol, 2 eq.), compound 2 was obtained as an oil after high vacuum.Yield: 500 mg, 1.18 mmol (10%).

¹H NMR (500 MHz, CDCl₃) δ 3.86 (4H, s), 3.55-3.49 (16H, m), 1.31 (9H,s). Analytical data matched those previously reported.³⁹

di-tert-butyl 3,6,9,12,15,18-hexaoxaicosanedioate (3)

Following general method A, from pentaethylene glycol (1.126 g, 1 ml,4.72 mmol, 1 eq.) in 10 ml of dioxane, NaH 60% in mineral oil (377 mg,9.45 mmol, 2 eq.) and tert-Butyl bromoacetate (1.872 g, 1.7 ml, 11.5mmol, 2 eq.), compound 3 was obtained as an oil after high vacuum.Yield: 300 mg, 0.641 mmol (14%).

¹H NMR (400 MHz, CDCl₃) δ 3.94 (4H, s), 3.66-3.56 (20H, m), 1.40 (18H,s). Analytical data matched those previously reported³⁹.

1-phenyl-2,5,8,11,14-pentaoxahexadecan-16-ol (9)

Pentaethylene glycol (9.53 g, 50 mmol, 5 eq.) was added dropwise to asuspension of NaH 60% in mineral oil (800 mg, 20 mmol, 2.5 eq.) in 20 mlof DMF at 0° C. The resulting mixture was stirred at r.t for 1 h. Thereaction mixture was cooled to 0° C., benzyl chloride (1 ml, 1.1 g, 8.72mmol, 1 eq.) was added. The resulting mixture was stirred O/N at r.t.The reaction was quenched with a saturated solution of NH₄Cl and theaqueous phase was extracted with ethyl acetate (×3). The combinedorganic phases were dried over MgSO₄ and evaporated to dryness. Theresulting oil was purified by column chromatography (from 0 to 60% ofethyl acetate in heptane) to afford the title compound as an oil. Yield:2.055 g, 6.25 mmol (71%).

¹H NMR (400 MHz, CDCl₃) δ 7.28-7.19 (5H, m), 4.50 (2H, s), 3.66-3.52(20H, m), 2.50 (1H, 5). ¹³C NMR (101 MHz, CDCl₃) 138.2, 128.3, 127.8,127.6, 73.2, 72.7, 70.61, 70.58, 70.53, 70.51, 70.2, 69.4, 61.7

tert-butyl 1-phenyl-2,5,8,11,14,17-hexaoxanonadecan-19-oate (10)

To a stirred solution of 9 (2.055 g, 6.25 mmol, 1 eq.) in 12.8 ml of DCMwas added 37% solution of NaOH (12.8 ml), followed by tert-butylbromoacetate (4.882 g, 25 mmol, 4 eq.) and TBABr (2118 mg, 6.37 mmol, 1.02eq.). The resulting solution was stirred O/N at r.t. The reactionmixture was extracted with ethyl acetate (×3). The organic phases werecombined and washed with brine (×1), dried over MgSO₄ and concentrate invacuo. The resulting brown oil was purified by column chromatography(from 0 to 30% of ethyl acetate in petroleum) to afford the titledcompound as colourless oil. Yield: 2.216 g, 5 mmol (80%).

¹H NMR (500 MHz, CDCl₃) δ 7.28-7.20 (5H, m), 4.50 (2H, s), 3.95 (2H, s),3.65-3.55 (20H, m), 1.40 (9H, s). ¹³C NMR (126 MHz, CDCl₃) δ169.7,128.4, 127.7, 127.6, 81.5, 73.2, 70.7, 70.7, 70.6, 70.6, 69.4, 69.1,28.1. HRMS (ESI) m/z: [M+H]⁺ calculated for: C₂₃H₃₈O₈: 442.26; observed:387.2.

19,19-dimethyl-17-oxo-3,6,9,12,15,18-hexaoxaicosanoic acid (11)

10 (2.216 g, 5 mmol, 1 eq.) was dissolved in 75 ml of ethanol, Pd/C (10wt %) was added and the resulting mixture was place under hydrogen andstirred at r.t. until complete conversion of the starting material. Thereaction mixture was filtered through celite, the celite pad was washedfew times using ethanol. The filtrate was concentrated in vacuum to givean oil that was used for the next step without further purification.Yield: 1.764 g, 5 mmol (quantitative).

BAIB (3.546 g, 11.01 mmol, 2.2 eq.) and TEMPO (171.87 mg, 1.10 mmol,0.22 eq.) were added to a solution of ACN/H₂O 1:1 containing previousobtained oil (1.764 g, 5 mmol, 1 eq.). The resulting mixture was stirredat r.t until complete conversion of the starting material. The crude waspurified using ISOLUTE® PE-AX anion exchange column. The column wasequilibrate with methanol, the reaction mixture poured in the column andlet it adsorbed in the pad. The column was washed with methanol (×3) toelute all the unbound material. Then, the titled product was elutedusing a 50% solution of formic acid in methanol. The organic phase wasevaporated to dryness to afford the title compound as oil. Yield: 1.200g, 3.27 mmol (65%).

¹H NMR (400 MHz, CDCl₃) δ, ppm 4.12 (2H, s), 3.98 (2H, s), 3.72-3.60(16H, m), 1.43 (9H, s). ¹³C NMR (101 MHz, CDCl₃) δ, ppm 172.6, 169.7,81.6, 71.0, 70.59, 70.56, 70.54, 70.46, 70.38, 70.35, 70.30, 68.9, 68.8,28.1.

3, 6,9,12-tetraoxatetradecane-1,14-diyl dimethanesulfonate (19)

Pentaethylene glycol (476.56 mg, 0.423 ml, 2 mmol, 1 eq.) was dissolvedin 4 ml of dry DCM. The temperature of the resulting mixture was cooleddown to 0° C. and methanesulfonyl chloride (687.3 mg, 0.464 ml, 16 mmol,3 eq.) was added followed by triethylamine (1011.9 g, 1.39 ml, 10 mmol,5 eq.). The resulting mixture was stirred at 0° C. for 4 h. A 10%aqueous solution of NaHSO₄ was added till pH=3. The aqueous phase wasextracted with DCM (×5). The organic phases were combined, dried overMgSO₄ and concentrated in vacuum to afford the title compound as anorange oil. Yield: 701 mg, 1.77 mmol (89%).

¹H NMR (400 MHz, CDCl₃) δ 4.33-4.30 (4H, m), 3.72-3.69 (4H, m),3.62-3.56 (12H, m), 3.02 (6H, s). Analytical data matched thosepreviously reported [Kimura et al. J. Polym. Sci. Part A: Polym. Chem.54, (2016).]

tert-butyl 17-((methylsulfonyl)oxy)-3,6,9,12,15-pentaoxaheptadecanoate(20)

10 (251 mg, 0.712 mmol, 1 eq.) was dissolved in 1.4 ml of dry DCM. Thetemperature of the resulting mixture was cooled down to 0° C. andmethanesulfonyl chloride (122.3 mg, 0.082 ml, 1.068 mmol, 1.5 eq.) wasadded followed by triethylamine (216.14 mg, 0.3 ml, 2.136 ml, 3 eq.).The resulting mixture was stirred at 0° C. for 4 h. A 10% aqueoussolution of NaHSO₄ was added till pH=3. The aqueous phase was extractedwith DCM (×5). The organic phases were combined, dried over MgSO₄ andconcentrated in vacuum to afford the title compound as a orange oil.Yield: 276 mg, 0.641 mmol (90%).

¹H NMR (400 MHz, CDCl₃) δ 4.32-4.30 (2H, m), 3.95 (2H, s), 3.71-3.57(18H, m), 3.02 (3H, s), 1.41 (9H, s). ¹³C NMR (101 MHz, CDCl₃) δ 169.7,81.5, 70.72, 70.65, 70.61, 70.58, 70.5, 69.3, 69.0, 37.7, 28.1.

tert-butyl(S)-19-((S,4R)-4-hydroxy-2-((4-(4-methylthiazol-5-yl))benzyl)carbamoyl)pyrrolidine-1-carbonyl)-20,20-dimethyl-17-oxo-3,6,9,12,15-pentaoxa-18-azahenicosanoate(12)

To a solution of PEG linker 11 (78.8 mg , 0.215 mmol, 1 eq.) in 1.5 mlDMF was added HATU (81.74 mg, 0.215 mmol, 1 eq.), HOAT (29.26 mg, 0.215mmol, 1 eq.), DIPEA and the solution was stirred at room temperature for5 min. Compound 7 (100 mg, 0.215 mmol, 1 eq.) was added and the pH ofthe reaction mixture was adjusted to >9 by addition of DIPEA(80.13 mg,0.106 ml, 0.645 mmol, 3 eq.). The mixture was stirred at roomtemperature until no presence of the starting materials was detected byLC-MS. The solvent was evaporated under reduced pressure to give thecorresponding crude, which was purified by HPLC using a gradient of 20%to 95% v/v acetonitrile in 0.1% aqueous solution of ammonia to yield thetitled compound as white solid. Yield: 75.6 mg, 0.094 mmol (44%).

¹H NMR (400 MHz, CDCl₃): δ ppm 9.00 (1H, s), 7.45 (1H, t, J=5.9 Hz),7.39-7.33 (4H, m), 7.29 (1H, d, J=8.9 Hz), 4.71 (1H, t, J=8.0 Hz),4.59-4.48 (3H, m), 4.34 (1H, dd, J=5.2, 14.6 Hz), 4.08-3.92 (5H, m),3.69-3.61 (18H, m), 2.52 (3H, s), 2.47-2.41 (1H, m), 2.19-2.11 (1H, m),1.46 (9H, s), 0.97 (9H, s). ¹³C NMR (101 MHz, CDCl₃) δ 171.3, 171.1,170.5, 170.0, 151.7, 139.1, 129.4, 128.3, 82.0, 71.1, 70.6, 70.4, 70.4,70.3, 70.3, 70.2, 70.2, 68.9, 58.7, 57.3, 56.8, 43.1, 36.3, 35.1, 28.1,26.4, 15.1. HRMS (ESI) m/z: [M+H]⁺ calculated for: C₃₈H₅₈N₄O₁₁S₂:778.38; observed: 779.4.

N¹—((R)-1-((2R,4R)-4-hydroxy-2-((4-(4-methylthiazol-5-yl)benzyl)carbamoyl)pyrrolidin-1-yl)-3,3-dimethyl-1-oxobutan-2-yl)-N¹⁷—((S)-1-((2S,4R)-4-hydroxy-2-((4-(4-methylthiazol-5-yl)benzyl)carbamoyl)pyrrolidin-1-yl)-3,3-dimethyl-1-oxobutan-2-yl)-3,6,9,12,15-pentaoxaheptadecanediamide(CMP99)

Following general method B, from compound 12 (75.6 mg, 0.094 mmol, 1eq.) and trifluoroacetic acid (1 ml in 1 ml of DCM), the carboxylic acidderivative was obtained as oil. The crude was used for the next stepwithout further purification. Yield: 70 mg, 0.094 mmol (quantitative).MS (ESI) m/z: [M+H]⁺ calculated for: C₃₄H₅₀N₄O₁₁S: 722.32; observed:723.3. Following general method B, from compound 13 (5.5 mg, 0.006 mmol,1 eq.), compound 8 (2.77 mg, 0.006 mmol, 1 eq.), HATU (2.28 mg, 0.0.006mmol, 1 eq.), HOAT (1 mg, 0.0.006 mmol, 1 eq.), DIPEA (2.23 mg, 0.002ml, 0.018 mmol, 3 eq.), CMP99 was obtained as a white solid. Yield: 4.5mg, 0.004 mmol (66%).

¹H NMR (400 MHz, CDCl3): d, ppm 8.74 (2H, d, J=2.8 Hz), 7.37-7.34 (9H,m), 7.18 (1H, d, J=8.9 Hz), 4.76-4.64 (3H, m), 4.59-4.44 (5H, m),4.37-4.26 (2H, m), 4.05-3.59 (27H, m), 2.52 (6H, s), 2.31-2.11 (4H, m),0.96 (9H, s), 0.95 (9H, s). HRMS (ESI) m/z: [M+H]⁺ calculated for:C₅₆H₇₈N₈O₁₃S₂: 1134.51; observed: 1135.58.

N¹,N¹⁴-bis((S)-1-((2S,4R)-4-hydroxy-2-((4-(4-methylthiazol-5-yl)benzyl)carbamoyl)pyrrolidin-1-yl)-3,3-dimethyl-1-oxobutan-2-yl)-3,6,9,12-tetraoxatetradecanediamide(CM09)

Following general method B, from compound 1 (6.80 mg, 0.018 mmol, 1eq.), compound 7 (20 mg, 0.045 mmol, 2.5 eq.), HATU (17 mg, 0.045 mmol,2.5 eq), HOAT (6.12, 0.045 mmol, 2.5 mmol), DIPEA (6.98 mg, 0.054 mmol,3 eq) compound CM09 was obtained as a white solid. Yield: 8 mg, 0.007mmol (40%).

¹H NMR (400 MHz, CDCl₃) δ 8.61 (2H, s), 7.48-7.45 (2H, m), 7.31-7.27(8H, m), 7.23 (2H, d, J=10.2 Hz), 4.64-4.59 (2H, m), 4.52-4.46 (4H, m),4.41-4.38 (2H, m), 4.31-4.25 (2H, m), 4.01-3.94 (4H, m), 3.82 (2H, d,J=15.7 Hz), 3.62-3.52 (12H, m), 2.45 (6H, s), 2.42-2.34 (2H, m),2.12-2.06 (2H, m), 1.19 (2H, s), 0.89 (18H, s); ¹³C NMR (101 MHz, CDCl₃)δ 170.2, 169.9, 169.6, 149.3, 147.5, 137.3, 130.6, 129.9, 128.4, 127.1,69.9, 69.5, 69.3, 69.1, 57.6, 56.1, 55.9, 42.2, 35.5, 34.6, 25.4, 15.1.HRMS (ESI) m/z: [M+H]⁺ calculated for: C₅₄H₇₄N₈O₁₂S₂: 1090.49; observed:1091.4.

N¹,N¹⁷-bis((S)-1-((2S,4R)-4-hydroxy-2-((4-(4-methylthiazol-5-yl)benzyl)carbamoyl)pyrrolidin-1-yl)-3,3-dimethyl-1-oxobutan-2-yl)-3,6,9,12,15-pentaoxaheptadecanediamide(CM10)

Following general method B, from compound 2 (7.60 mg, 0.018 mmol, 1eq.), compound 7 (20 mg, 0.045 mmol, 2.5 eq.), HATU (17 mg, 0.045 mmol,2.5 eq), HOAT (6.12, 0.045 mmol, 2.5 mmol), DIPEA (6.98 mg, 0.054 mmol,3 eq) compound CM10 was obtained as a white solid. Yield: 6 mg, 0.005mmol (30%).

¹H NMR (400 MHz, MeOD) δ 9.28 (2H, s), 7.43-7.36 (10H, m), 5.39 (2H, s),4.77 (10H, s), 4.59 (2H, s), 4.50-4.43 (4H, m), 4.42-4.38 (2H, m), 4.26(2H, d, J=17.2 Hz), 3.96-3.92 (4H, m), 3.77 (2H, d, J=11.1 Hz),3.73-3.68 (2H, m), 3.56 (16H, m), 3.22-3.20 (10H, m), 2.43 (6H, s),2.16-2.14 (2H, m), 2.13 (2H, m), 2.02-1.95 (2H, m); ¹³C NMR (101 MHz,CDCl₃) δ 173.1, 172.4, 170.7, 170.3, 153.3, 153.2, 144.5, 140.0, 134.0,129.2, 129.0, 128.4, 128.3, 127.8, 70.9, 70.5, 70.2, 70.1, 69.7, 68.2,67.7, 59.7, 59.4, 56.8, 56.7, 54.9, 42.9, 42.3, 39.9, 37.6, 36.3, 35.7,34.7, 25.6, 25.5, 13.1. HRMS (ESI) m/z: [M+H]⁺ calculated for:C₅₆H₇₈N₈O₁₃S₂: 1134.51; observed: 1135.55.

N¹,N²⁰-bis((S)-1-((2S,4R)-4-hydroxy-2-((4-(4-methylthiazol-5-yl)benzyl)carbamoyl)pyrrolidin-1-yl)-3,3-dimethyl-1-oxobutan-2-yl)-3,6,9,12,15,18-hexaoxaicosanediamide(CM11)

Following general method B, from compound 3 (8.39 mg, 0.018 mmol, 1eq.), compound 7 (20 mg, 0.045 mmol, 2.5 eq.), HATU (17 mg, 0.045 mmol,2.5 eq), HOAT (6.12, 0.045 mmol, 2.5 mmol), DIPEA (6.98 mg, 0.054 mmol,3 eq) compound CM11 was obtained as a white solid. Yield: 11.74 mg,0.0099 mmol (55%).

¹H NMR (400 MHz, CDCl₃) δ 8.61 (2H, s), 7.41-7.38 (2H, m), 7.29 (10H, t,J=7.6 Hz), 4.66-4.61 (2H, m), 4.49-4.41 (6H, m), 4.35-4.29 (2H, m),3.98-3.91 (6H, m), 3.62-3.50 (24H, m), 2.45 (6H, s), 2.42-2.35 (2H, m),2.11-2.06 (2H, m), 0.88 (18H, s); ¹³C NMR (101 MHz, CDCl₃) δ 171.2,170.9, 170.4, 150.3, 148.5, 138.3, 131.6, 130.9, 129.5, 128.1, 71.2,70.61, 70.59, 70.5, 70.4, 70.3, 58.6, 57.0, 43.2, 36.5, 35.6, 26.4,16.1. HRMS (ESI) m/z: [M+H]⁺ calculated for: C₅₈H₈₂N₈O₁₄S₂: 1178.54;observed: 1179.60.

N¹,N²⁰-bis((S)-1-((2S,4S)-4-hydroxy-2-((4-(4-methylthiazol-5-yl)benzyl)carbamoyl)pyrrolidin-1-yl)-3,3-dimethyl-1-oxobutan-2-yl)-3,6,9,12,15,18-hexaoxaicosanediamide(CMP98)

Following general method B, from compound 3 (7.12 mg, 0.028 mmol, 1eq.), compound 8 (18.06, 0.040 mmol, 2.1 eq.), HATU (15.2 mg, 0.040mmol, 2 eq.), HOAT (5.44 mg, 0.040 mmol, 2 eq.), DIPEA (7.45 mg, 0.0010ml, 3 eq.), compound CMP98 was obtained as a white solid. Yield: 10.58mg, 0.0089 mmol (45%).

¹H NMR (400 MHz, CDCl₃) δ 9.09 (2H, s), 8.02 (2H, s), 7.31 (4H, d, J=8.5Hz), 7.22 (4H, d, J=8.0 Hz), 7.16 (2H, d, J=9.2 Hz), 4.75-4.64 (4H, m),4.51 (2H, d, J=8.9 Hz), 4.41-4.37 (2H, m), 4.24-4.17 (2H, m), 3.94 (4H,d, J=3.2 Hz), 3.84-3.81 (4H, m), 3.62-3.54 (20H, m), 2.49-2.47 (2H, m),2.44 (6H, s), 2.26-2.17 (4H, m), 0.93 (18H, s); ¹³C NMR (101 MHz, CDCl₃)δ 173.2, 171.5, 169.7, 151.8, 138.8, 132.9, 129.5, 129.2, 128.3, 71.2,71.1, 70.6, 70.48, 70.45, 70.4, 70.3, 59.9, 58.5, 56.5, 43.2, 35.6,35.2, 26.4, 15.0. HRMS (ESI) m/z: [M+H]⁺ calculated for: C₅₈H₈₂N₈O₁₄S₂:1178.54; observed: 1179.60.

(2S,2′S,4R,4′R)—N,N′-((((3,6,9,12-tetraoxatetradecane-1,14-diyl)bis(oxy))bis(4-(4-methylthiazol-5-yl)-2,1-phenylene))bis(methylene))bis(1-((S)-2-(1-cyanocyclopropane-1-carboxamido)-3,3-dimethylbutanoyl)-4-hydroxypyrrolidine-2-carboxamide)(CMP108)

Following general method C, from 18 (27 mg, 0.05 mmol, 2 eq.), 19 (11.83mg, 0.03 mmol, 1.2 eq.) and K₂CO₃ (41.46 mg, 0.3 mmol, 6 eq.), thetitled compound was obtained as a white solid. Yield: 9.1 mg, 0.007 mmol(28%).

¹H NMR (400 MHz, CDCl₃) δ 8.61 (2H, s), 7.41-7.38 (2H, m), 7.26 (2H, d,J=8.1 Hz), 7.00 (2H, d, J=8.1 Hz), 6.91-6.88 (2H, m), 6.85-6.81 (2H, m),4.57-4.52 (2H, m), 4.44-4.36 (8H, m), 4.19-4.08 (4H, m), 3.89-3.53 (22H,m), 2.45 (6H, s), 2.24-2.17 (2H, m), 2.08-2.02 (2H, m), 1.61-1.37 (8H,m), 0.88 (18H, s); ¹³C NMR (101 MHz, CDCl₃) δ 170.9, 170.0, 165.4,156.9, 150.4, 148.5, 132.3, 131.7, 130.0, 126.9, 122.0, 119.6, 112.9,70.7, 70.41, 70.38, 70.2, 69.6, 67.9, 58.9, 58.4, 56.6, 39.2, 37.0,36.0, 26.3, 17.9, 17.7, 16.2, 13.7. HRMS (ESI) m/z: [M+H]⁺ calculatedfor: C₆₄H₈₄N₁₀O₁₄S₂: 1280.56; observed: 1281.66.

(2S,2′S,4R,4′R)—N,N′-((((3,6,9,12-tetraoxatetradecane-1,14-diyl)bis(oxy))bis(4-(4-methylthiazol-5-yl)-2,1-phenylene))bis(methylene))bis(1-((S)-2-acetamido-3,3-dimethylbutanoyl)-4-hydroxypyrrolidine-2-carboxamide)(CMP106)

Following general method C, from 17 (24.3 mg, 0.05 mmol, 2 eq.), 19(11.83 mg, 0.03 mmol, 1.2 eq.) and and K₂CO₃ (41.46 mg, 0.3 mmol, 6eq.), the title compound was obtained as a white solid. Yield: 7.8 mg,0.006 mmol (26%).

¹H NMR (400 MHz, CDCl₃) δ 8.60 (2H, s), 7.39-7.35 (2H, m), 7.26 (2H, d,J=7.6 Hz), 6.91-6.88 (2H, m), 6.83-6.80 (2H, m), 6.36-6.13 (2H, m),4.60-4.32 (10H, m), 4.18-4.05 (4H, m), 3.97-3.79 (6H, m), 3.71-3.54(18H, m), 2.44 (6H, s), 2.17-1.86 (8H, m), 0.87 (18H, s); ¹³C NMR (101MHz, CDCl₃) δ 171.3, 171.1, 171.0, 170.7, 170.5, 156.8, 156.8, 150.3,148.5, 132.2, 131.7, 130.0, 129.8, 127.1, 126.9, 122.1, 122.0, 112.8,112.8, 71.3, 70.7, 70.6, 70.5, 70.5, 70.5, 70.4 , 70.2, 70.1, 69.7,67.9, 58.9, 58.6, 57.6, 57.5, 56.9, 56.7, 42.7, 39.1, 39.0, 37.1, 36.4,35.4, 35.1, 26.4, 26.4, 23.2, 23.1, 16.2. HRMS (ESI) m/z: [M+H]⁺calculated for: C₅₈H₈₂N₈O₁₄S₂: 1178.54; observed: 1281.66.

tert-butyl(14-(2-(((2S,4R)-1-((S)-2-(1-cyanocyclopropane-1-carboxamido)-3,3-dimethylbutanoyl)-4-hydroxypyrrolidine-2-carboxamido)methyl)-5-(4-methylthiazol-5-yl)phenoxy)-3,6,9,12-tetraoxatetradecyl)carbonate (22)

Following general method C, from 18 (27 mg, 0.05 mmol, 1 eq.), 20 (26mg, 0.06 mmol, 1.2 eq.) and K₂CO₃ (20.73 mg, 0.15 mmol, 3 eq.), thetitle compound was obtained as a white solid. Yield: 17 mg, 0.02 mmol(33%).

¹H NMR (400 MHz, CDCl₃) δ 8.61 (1H, s), 7.33-7.25 (2H, m), 6.97 (1H, d,J=9.1 Hz), 6.92-6.89 (1H, m), 6.84 (1H, d, J=1.5 Hz), 4.59-4.55 (1H, m),4.45-4.38 (4H, m), 4.22-4.10 (2H, m), 3.93-3.54 (24H, m), 2.46 (3H, s),2.32-2.24 (1H, m), 2.10-2.04 (1H, m), 1.63-1.52 (2H, m), 1.45-1.39 (12H,m), 0.87 (9H, s); ¹³C NMR (101 MHz, CDCl₃) δ 170.6, 170.1, 169.7, 165.4,156.9, 150.3, 148.5, 132.3, 131.7, 130.0, 126.9, 122.0, 119.7, 112.9,81.7, 70.72, 70.66, 70.5, 70.4, 70.3, 69.6, 69.0, 68.0, 58.8, 58.4,56.6, 39.3, 36.7, 35.8, 28.1, 26.3, 17.8, 16.2, 13.7. HRMS (ESI) m/z:[M+H]⁺ calculated for: C₄₃H₆₃N₅O₁₂S: 873.42; observed: 874.49.

tert-butyl17-(2-(((2S,4R)-1-((S)-2-acetamido-3,3-dimethylbutanoyl)-4-hydroxypyrrolidine-2-carboxamido)methyl)-5-(4-methylthiazol-5-yl)phenoxy)-3,6,9,12,15-pentaoxaheptadecanoate(21)

Following general method C, from 17 (24.3 mg, 0.05 mmol, 1 eq.), 20 (26mg, 0.06 mmol, 1.2 eq.) and K₂CO₃ (20.73 mg, 0.15 mmol, 3 eq.), thetitle compound was obtained as a white solid. Yield: 17 mg, 0.021 mmol(33%).

¹H NMR (400 MHz, CDCl₃) δ, ppm 8.67 (1H, s), 7.32 (2H, d, J=7.8 Hz),6.95 (1H, dd, J=1.6, 7.6 Hz), 6.88 (1H, d, J=1.8 Hz), 4.65-4.60 (1H, m),4.53-4.43 (2H, m), 4.39-4.36 (1H, m), 4.24-4.13 (2H, m), 4.00 (2H, d,J=7.0 Hz), 3.92-3.87 (2H, m), 3.77-3.59 (20H, m), 3.08 (2H, s), 2.51(3H, s), 2.38-2.31 (1H, m), 1.98 (3H, s). ¹³C NMR (101 MHz, CDCl₃) δ171.2, 170.8, 170.4, 169.7, 156.8, 150.3, 148.5, 132.2, 131.7, 129.8,126.9, 122.0, 112.8, 81.6, 70.8, 70.71, 70.69, 70.60, 70.57, 70.55,70.52, 70.49, 70.47, 70.1, 69.6, 69.3, 69.02, 68.98, 67.9, 58.6, 57.5,56.7, 39.0, 37.7, 36.5, 35.2, 28.1, 26.4, 23.2, 16.1. HRMS (ESI) m/z:[M+H]⁺ calculated for: C₄₀H₆₂N₄O₁₂S: 822.41; observed: 823.5.

(2S,4R)-1-((S)-2-(tert-butyl)-20-(2-(((2S,4R)-1-((S)-2-(1-cyanocyclopropane-1-carboxamido)-3,3-dimethylbutanoyl)-4-hydroxypyrrolidine-2-carboxamido)methyl)-5-(4-methylthiazol-5-yl)phenoxy)-4-oxo-6,9,12,15,18-pentaoxa-3-azaicosanoyl)-4-hydroxy-N-(4-(4-methylthiazol-5-yl)benzyl)pyrrolidine-2-carboxamide(CMP113)

Following general method B, from compound 20 (17 mg, 0.02 mmol, 1 eq.)and trifluoroacetic acid (0.5 ml in 0.5 ml of DCM), the carboxylic acidderivative was obtained as an oil. Yield: 15.7 mg, 0.019 mmol(quantitative). HRMS (ESI) m/z: [M+H]⁺ calculated for: C₃₉H₅₅N₅O₁₂S:817.36; observed: 818.4.

From the obtained carboxylic acid (15.7 mg, 0.019 mmol, 1 eq.) in 0.5 mlDMF, HATU (7.22 mg, 0.019 mmol, 1 eq.), HOAT (2.58 mg, 0.019 mmol, 1eq.), compound 7 (8.73 mg, 0.019 mmol, 1 eq.) and DIPEA (3 eq.), thefinal compound was isolated as white solid. Yield: 6.3 mg, 0.005 mmol(27%).

¹H NMR (400 MHz, CDCl₃) δ 8.61 (2H, s), 7.58-7.54 (1H, m), 7.31-7.25(5H, m), 7.02 (1H, d, J=9.7 Hz), 6.88-6.85 (1H, m), 6.78 (1H, d, J=1.5Hz), 4.59-4.56 (2H, m), 4.47-4.25 (6H, m), 4.13-3.52 (20H, m), 2.47-2.42(6H, m), 2.34-2.27 (1H, m), 2.19-2.03 (5H, m), 1.63-1.52 (2H, m),1.48-1.37 (2H, m), 0.90 (18H, s); ¹³C NMR (101 MHz, CDCl₃) δ 171.2,171.1, 170.7, 170.3, 165.4, 156.6, 150.3, 148.4, 148.3, 138.3, 132.0,131.8, 131.7, 130.7, 129.5, 129.4, 127.9, 126.9, 122.0, 119.7, 112.6,71.0, 70.7, 70.5, 70.4, 70.32, 70.28, 70.25, 69.6, 67.9, 59.1, 58.8,58.5, 57.3, 57.1, 56.7, 43.1, 39.0, 37.3, 36.8, 36.2, 35.4, 26.4, 26.3,17.9, 17.7, 16.1, 16.0, 13.7. HRMS (ESI) m/z: [M+H]⁺ calculated for:C₆₁H₈₃N₉O₁₄S₂: 1229.55; observed: 1230.66.

(2S,4R)-1-((S)-2-acetamido-3,3-dimethylbutanoyl)-4-hydroxy-N-(2-((S)-19-((2S,4R)-4-hydroxy-2-((4-(4-methylthiazol-5-yl)benzyl)carbamoyl)pyrrolidine-1-carbonyl)-20,20-dimethyl-17-oxo-3,6,9,12,15-pentaoxa-18-azahenicosyl)oxy)-4-(4-methylthiazol-5-yl)benzyl)pyrrolidine-2-carboxamide(CMP112)

Following general method B, from compound 20 (17 mg, 0.021 mmol, 1 eq.)and trifluoroacetic acid (0.5 ml in 0.5 ml of DCM), the carboxylic acidderivative or 38 was obtained as an oil. Yield: 13 mg, 0.017 mmol(quantitative). HRMS (ESI) m/z: [M+H]⁺ calculated for: C₃₆H₅₄N₄O₁₂S:766.35; observed: 767.4.

From the carboxylic acid (13 mg, 0.017 mmol, 1 eq.) in 0.5 ml DMF, HATU(6.49 mg, 0.017 mmol, 1 eq.), HOAT (2.31 mg, 0.017 mmol, 1 eq.),compound 7 (7.90 mg, 0.017 mmol, 1 eq.) and DIPEA (3 eq.)the titledcompound was obtained as a white solid. Yield: 6 mg, 0.005 mmol (30%).

¹H NMR (400 MHz, CDCl₃) δ 8.61 (2H, s), 7.49-7.45 (1H, m), 7.32-7.24(6H, m), 6.90-6.87 (1H, m), 6.79 (1H, d, J=2.4 Hz), 6.24 (1H, d, J=8.9Hz), 4.61-4.29 (10H, m), 4.11-3.52 (27H, m), 2.44 (6H, s), 2.30 (1H, t,J=13.3 Hz), 2.18-2.03 (3H, m), 0.87 (9H, s); ¹³C NMR (101 MHz, CDCl₃) δ171.2, 171.1, 170.7, 170.4, 156.7, 150.3, 148.4, 138.3, 132.2, 130.9,129.7, 129.4, 128.0, 127.0, 122.0, 112.8, 70.9, 70.6, 70.5, 70.4, 70.3,70.2, 69.6, 67.9, 59.0, 58.8, 57.7, 57.1, 43.1, 39.0, 37.1, 36.8, 35.6,35.5, 26.42, 26.38, 23.0, 16.13, 16.06. HRMS (ESI) m/z: [M+H]⁺calculated for: C₅₈H₈₂N₈O₁₄S₂: 1178.54; observed: 1179.6.

General Method D:

To a solution of the diol (1 eq.) in DCM, tert-butyl bromoacetate (8eq.), TBABr (1.1 eq.) and 37% w/w aqueous NaOH were added. The reactionmixture was vigorously stirred at r.t. overnight. The organic phase wasseparated from the aqueous layer and then the aqueous phase wasextracted with DCM (×3). Organic layers were collected, dried over MgSO₄and evaporated under reduced pressure. The crude was purified by flashchromatography eluting with ethyl acetate from 10% to 50% v/v inheptane.

General Method E:

A solution of the benzylated starting material in absolute EtOH (0.05 M)was flown in an H-cube machine at a rate of 1 mL/min, H₂ 10 atm, 70° C.Solvent was evaporated under reduced pressure to yield the finalcompound.

General Method F:

To a solution of the dicarboxylic acid linker (1 eq.) in dry DMF, COMU(2 eq.) and DIPEA (5 eq.) were added. The solution was stirred for 10min and then it was added to a suspension of the VHL-ligand amine 7 (2.1eq.) and DIPEA (5 eq.) in dry DMF. The mixture was stirred at r.t. untilno presence of the starting material was detected by LC-MS. Ice wasadded and the volatiles were evaporated under reduced pressure to givethe crude which was purified by HPLC using a gradient of 20% to 70% v/vacetonitrile in 0.1% v/v aqueous solution of formic acid to yield thefinal compound.

4,4′-(Butane-1,4-diylbis(oxy))bis(butan-1-ol) (101)

Compound 101 was prepared as reported⁴⁰ by Knuf et al. Analytical datamatched those previously reported.

Di-tert-butyl 3,8,13,18-tetraoxaicosanedioate (102)

Prepared following the general method D from compound 101 (198 mg,0.8449 mmol) in 37% w/w aqueous NaOH (4 mL) and DCM (4 mL). Compound 102was obtained as an oil (158 mg, yield: 40%).

¹H-NMR (400 MHz, CDCl₃) δ: 3.87(4H, s), 3.45 (4H, t, J=6.1 Hz),3.38-3.30 (8H, m), 1.67-1.51 (12H, m), 1.41 (18H, s).

3,8,13,18-Tetraoxaicosanedioic acid (103)

Prepared following the general method B starting from compound 102 (158mg, 0.3415 mmol) in TFA/DCM 1:1 (2 mL). Compound 103 was obtained as anoil (120 mg, yield: quantitative).

¹H-NMR (400 MHz, CDCl₃) δ: 8.26 (s, 2H), 4.09 (s, 4H), 3.58 (t, J=6.1Hz, 4H), 3.48-3.41 (m, 8H), 1.75-1.60 (m, 12H).¹³C-NMR (101 MHz, CDCl₃)δ: 173.1, 71.7, 70.6, 70.4, 67.9, 26.4, 26.3, 26.1.

5-(Benzyloxy)pentan-1-ol (104)

1,5-Pentandiol (3.430 g, 3.45 mL, 0.033 mol, 4 eq.) was added dropwiseto a suspension of NaH (670 mg, 0.016 mol, 2 eq) in DMF (14 mL) at 0° C.A catalytic amount of Nal was added, followed by benzylbromide (1.360 g,0.95 mL, 0.008 mol, 1 eq.). The mixture was stirred at r.t. overnight.

The reaction was quenched with NH₄Cl aq. sat. and then extracted withethyl acetate (×3).

Organic layers were collected and evaporated under reduced pressure. Thecrude was purified by flash chromatography eluting from 40% to 90% ofethyl acetate in heptane to give the desired product (1.08 g, yield:70%).

Analytical data matched those previously reported.⁴¹

2-(2-(2-(Benzyloxy)ethoxy)ethoxy)ethyl methanesulfonate (105)

Compound 105 was obtained following the method previously reported^(.42)Analytical data matched those reported.

1,18-Diphenyl-2,5,8,11,17-pentaoxaoctadecane (106)

Compound 104 (228.58 mg, 1.177 mmol, 2.5 eq) was added to a solution ofNaHMDS 1M in THF (107.95 mg, 0.588 mL, 0.588 mmol, 1.25 eq.) at 0° C.under N₂ atmosphere. Reaction mixture was stirred at r.t. for 1 h. Afterthis time a solution of compound 105 (150.00 mg, 0.471 mmol, 1 eq.) inDMF was added and the mixture was irradiated with microwave at 130° C.for 2 h.

After this time the solvent was evaporated, the reaction quenched with5% aqueous NaHSO₄ and extracted with DCM (×3). Organic layers werecollected, dried over MgSO₄, filtered and evaporated under reducedpressure. The crude was purified by flash chromatography eluting from 0%to 50% v/v of ethyl acetate in heptane to yield the desired compound 106as an oil (114 mg, yield: 58%).

¹H-NMR (500 MHz, CDCl₃) δ: 7.28-7.19 (m, 10H), 4.49 (s, 2H), 4.43 (s,2H), 3.62-3.54 (m, 10H), 3.51-3.48 (m, 2H), 3.43-3.36 (m, 4H), 1.61-1.48(m, 4H), 1.42-1.31 (m, 2H).

Di-tert-butyl 3,6,9,12,18-pentaoxaicosanedioate (107)

Starting from compound 106 (265 mg, 0.610 mmol) and following thegeneral method E the deprotected compound was obtained as an oil (131mg) and used without any further purification for the next step.

Following the general method D from the deprotected compound (131 mg,0.5544 mmol) in 37% w/w aqueous NaOH (2.2 mL) and DCM (2.2 mL) compound107 was obtained as an oil (122 mg, yield: 47%).

¹H-NMR (500 MHz, CDCl₃) δ: 4.00 (s, 2H), 3.92 (s, 2H), 3.69-3.60 (m,10H), 3.57-3.53 (m, 2H), 3.52-3.46 (m, 2H), 3.43 (t, J=7.1 Hz, 2H),1.67-1.56 (m, 4H), 1.46 (d, J=0.6 Hz, 18H), 1.43-1.37 (m, 2H). ¹³C-NMR(101 MHz, CDCl₃) δ: 169.8, 81.5, 81.4, 71.6, 71.3, 70.7, 70.6, 70.1,69.0, 68.8, 29.5, 29.4, 28.1, 22.6.

3,6,9,12,18-Pentaoxaicosanedioic acid (108)

Prepared following the general method B starting from compound 107 (90mg, 0.1937 mmol) in 2 mL of TFA/DCM 1:1. Compound 108 was obtained as anoil (66 mg, yield: quantitative).

¹H-NMR (400 MHz, CDCl₃) δ: 8.15 (s, 2H), 4.11 (s, 2H), 4.02 (s, 2H),3.71-3.40 (m, 16H), 1.65-1.52 (m, 4H), 1.43-1.34 (m, 2H)

1,5-Bis(allyloxy)pentane (109)

Compound 109 was obtained starting from 1,5-petandiol (500 mg, 4.8 mmol)and following the method reported.⁴³

Analytical data matched those previously reported.

3,3′-(Pentane-1,5-diylbis(oxy))bis(propan-1-ol) (110)

A solution of compound 109 (500 mg, 2.71 mmol, 1 eq.) in dry THF (4.2mL) was added dropwise to a solution 0.5 M of 9-Borabicyclo[3.3.1]nonanein THF (993 mg, 16.28 mL, 8.14 mmol, 3eq.) at 0° C. and the resultingsolution was stirred at r.t. overnight.

The reaction was quenched by MeOH (3.17 mL), 30% w/w aq. NaOH (6.35 mL),30% v/v aq. H₂O₂ (6.35 mL) and the mixture was left to stir for 2 h.Then it was extracted with ethyl acetate (×3). Organic layers werecollected, washed with brine, dried over MgSO₄ and evaporated underreduced pressure. The crude was purified by flash chromatography elutingfrom 0% to 100% ethyl acetate in heptane to yield the desired product asan oil (483 mg, yield: 81%). Analytical data matched those previouslyreported.⁴³

Di-tert-butyl 3,7,13,17-tetraoxanonadecanedioate (111)

Compound 111 was obtained from compound 110 (214 mg, 0.9714 mmol)following the general method D, in 37% w/w aqueous NaOH (4 mL) and DCM(4 mL). The desired product was obtained as an oil (65 mg, yield: 15%).

¹H-NMR (400 MHz, CDCl₃) δ: 3.88 (s, 4H), 3.53 (t, J=6.5 Hz, 4H), 3.44(t, J=6.4 Hz, 4H), 3.34 (t, J=6.9 Hz, 4H), 1.85-1.78 (m, 4H), 1.55-1.47(m, 4H), 1.41 (s, 18H), 1.36-1.29 (m, 2H).

3,7,13,17-Tetraoxanonadecanedioic acid (112)

Prepared following the general method B starting from compound 111 (64mg, 0.1427 mmol) in TFA/DCM 1:1 (2 mL). Compound 112 was obtained as anoil (47.5 mg, yield: quantitative).

¹H-NMR (400 MHz, CDCl₃) δ: 8.11 (s, 2H), 4.06 (s, 4H), 3.64 (t, J=5.9Hz, 4H), 3.54 (t, J=5.9 Hz, 4H), 3.42 (t, J=6.4 Hz, 4H), 1.88-1.81 (m,4H), 1.60-1.52 (m, 4H), 1.36 (dt, J=7.6, 11.9 Hz, 2H). ¹³C-NMR (101 MHz,CDCl₃) δ: 173.3, 71.1, 69.6, 68.2, 67.9, 29.4, 29.2, 22.7.

5-(Benzyloxy)pentyl 4-methylbenzenesulfonate (113)

To a solution of compound 104 (1.910 g, 9.8387 mmol, 1 eq.) andtriethylamine (1.65 mL, 11.8226 mmol, 1.2 eq.) in DCM (15 mL) a solutionof p-TsCl (2.063 g, 10.8226 mmol, 1.1 eq.) in DCM (15 mL) was added at0° C. The mixture was left to stir overnight. Then NaHCO₃ aq. sat. wasadded. The aqueous phase was separated from the organic layer and it wasextracted with DCM (×2). Organic layers were collected and washed with5% aqueous HCl solution. The crude was purified by flash chromatographyeluting from 0% to 60% v/v ethyl acetate in heptane to yield the desiredproduct (1.9 g, yield: 55%). Analytical data matched those previouslyreported.⁴⁴

1,18-Diphenyl-2,8,11,17-tetraoxaoctadecane (114)

A mixture of compound 113 (1.9 g, 5.6863 mmol, 2.4 eq.), ethylenglycol(147 mg, 2.3696 mmol, 1 eq.) and TBA bisulphate (804 mg, 2.3693 mmol, 1eq) was dissolved in toluene (8 mL) and NaOH aq. 50% (6 mL). The mixturewas vigorously stirred overnight. The organic phase was separated fromthe aqueous layer and then it was extracted with ethyl acetate (×3).Organic layers were collected, dried over MgSO₄ and evaporated underreduced pressure. The crude was purified by flash chromatography elutingwith a mixture v/v of ethyl acetate in heptane, from 100% heptane to100% ethyl acetate. The desired compound was obtained as an oil (200 mg,yield: 8.5%).

¹H-NMR (500 MHz, CDCl₃) δ: 7.25-7.22 (m, 10H), 4.40 (s, 4H), 3.47 (s,4H), 3.39-3.35 (m, 8H), 1.58-1.47 (m, 8H), 1.37-1.29 (m, 4H).

5,5′-(Ethane-1,2-diylbis(oxy))bis(pentan-1-ol (115)

Starting from compound 114 (200 mg, 0.8535 mmol) and following thegeneral method E compound 115 was obtained as an oil (35 mg, yield:31%).

¹H-NMR (400 MHz, CDCl₃) δ: 3.53 (t, J=6.1 Hz, 4H), 3.49 (s,4H), 3.49 (s,4H), 3.40 (t, J=6.6 Hz,4H), 2.93(s, 2H), 1.58-1.45(m, 8H), 1.37-1.29 (m,4H).

1,2-Di(1,3-dioxan-2-yl)ethane (118)

Compound 118 was prepared in accordance with the published procedure,⁴⁵starting from 2,5-dimethoxytetrahydrofuran (10.0 g, 75.6659 mmol).Analytical data matched those previously reported.

3,3′-(Butane-1,4-diylbis(oxy))bis(propan-1-ol) (119)

Compound 119 was prepared accordingly in accordance with the publishedprocedure,⁴⁵ starting from compound 118. Analytical data matched thosepreviously reported.

1-Phenyl-2,5,9,14-tetraoxaheptadecan-17-ol (120)

Compound 120 (1.1 g, 5.3325 mmol, 3 eq.) was dissolved in toluene (10mL) and NaOH aq. 50% w/w (5 mL). TBABr (590 mg, 1.7775 mmol, 1 eq.), acatalytic amount of TBAI and benzyl-2-bromoethyl ether (382 mg, 1.7775mmol, 1 eq.) were added and the reaction mixture was vigorously stirredfor 48 h. Organic layer was separated from the aqueous phase and theaqueous phase was extracted with DCM (×3). The crude was purified byflash chromatography eluting from 0% to 5% v/v MeOH in DCM to obtain theproduct as an oil (350 mg, 57%).

¹H-NMR (400 MHz, CDCl₃) δ: 7.33-7.22 (m, 5H), 4.55 (s, 2H), 3.74 (dd,J=5.7, 11.2 Hz, 2H), 3.59-3.55 (m, 6H), 3.53 (t, J=6.5 Hz, 2H), 3.47 (t,J=6.4 Hz, 2H), 3.44-3.37 (m, 4H), 2.44 (t, J=5.7 Hz, 1H), 1.87-1.76 (m,4H), 1.61-1.57 (m, 4H).

3-(4-(3-(2-Hydroxyethoxy)propoxy)butoxy)propan-1-ol (121)

The product was obtained starting from compound 120 (350 mg, 1.028 mmol)and following the general method E. The conversion was not quantitativeso the product 121 was separated from the starting material by a flashchromatography eluting from 100% DCM to 9:1 v/v DCM/MEOH (87 mg, yield:34%).

¹H-NMR (400 MHz, CDCl3) δ: 3.66-3.60 (m, 4H), 3.51-3.38 (m, 8H),3.38-3.31 (m, 4H), 1.79-1.69 (m, 4H), 1.57-1.50 (m, 4H).

Di-tert-butyl 3,6,10,15,19-pentaoxahenicosanedioate (122)

Compound 122 was obtained from compound 121 (87 mg, 0.3475 mmol)following the general method D, in 37% w/w aqueous NaOH (1.5 mL) and DCM(1.5 mL). The desired product was obtained as an oil (47 mg, yield:28%).

¹H-NMR (400 MHz, CDCl₃) δ: 3.99 (s, 2H), 3.68-3.42 (m, 12H), 3.41-3.36(m, 4H), 1.88-1.77 (m, 4H), 1.59-1.55 (m, 4H), 1.44 (s, 18H).

3,6,10,15,19-Pentaoxahenicosanedioic acid (123)

Prepared following the general method B starting from compound 122 (47mg, 0.0983 mmol) in TFA/DCM 1:1 (1 mL). Compound 123 was obtained as anoil (35 mg, yield: quantitative). ¹H-NMR (500 MHz, CDCl3) δ: 4.14 (s,2H), 4.07 (s, 2H), 3.73-3.69 (m, 2H), 3.65-3.59 (m, 4H), 3.59-3.53 (m,4H), 3.49 (t, J=6.3 Hz, 2H), 3.47-3.40 (m, 4H), 1.89-1.81 (m, 4H),1.62-1.57 (m, 4H).

13C-NMR (101 MHz, CDCl3) δ: 173.9, 173.7, 71.3, 71.0, 70.8, 70.0, 69.6,68.7, 68.6, 68.1, 68.0, 67.6, 29.7, 29.5, 26.3, 26.2.

N1,N20-Bis((S)-1-((2S,4R)-4-hydroxy-2-((4-(4-methylthiazol-5-yl)benzyl)carbamoyl)pyrrolidin-1-yl)-3,3-dimethyl-1-oxobutan-2-yl)-3,6,9,12,18-pentaoxaicosanediamide(124)

Compound 124 was prepared accordingly to general method F, starting fromcompound 7 (20 mg, 0.0428 mmol) and compound 108 (7.2 mg, 0.02038 mmol).5 mg were obtained (yield: 21%).

¹H-NMR (500 MHz, MeOD) δ: 8.77 (s, 2H), 7.34 (dd, J=7.4, 23.2 Hz, 8H),4.59 (dd, J=2.4, 9.4 Hz, 2H), 4.50-4.38 (m, 6H), 4.27 (t, J=4.3 Hz, 1H),4.24 (t, J=4.3 Hz, 1H), 3.94 (dd, J=15.3, 22.3 Hz, 2H), 3.85 (dd,J=15.3, 24.4 Hz, 2H), 3.76 (d, J=10.7 Hz, 2H), 3.72-3.68 (m, 2H),3.61-3.40 (m, 14H), 3.35 (dt, J=1.0, 6.5 Hz, 2H), 2.37 (s, 6H),2.16-2.09 (m, 2H), 2.02-1.96 (m, 2H), 1.57-1.45 (m, 4H), 1.39-1.32 (m,2H), 0.94 (s, 18H).

¹³C-NMR (101 MHz, MeOD) δ: 174.4, 174.3, 172.1, 172.0, 171.7, 152.9,149.0, 140.3, 133.4, 131.5, 130.5, 130.4, 129.5, 129.0, 72.9, 72.3,72.2, 71.7, 71.6, 71.5, 71.2, 71.1, 70.7, 60.8, 58.1, 58.0, 43.7, 38.9,37.2, 37.1, 30.5, 30.4, 27.0, 26.9, 23.8, 15.8.

HRMS: found 1177.6435 [M+H⁺].

N1,N20-Bis((S)-1-((2S,4R)-4-hydroxy-2-((4-(4-methylthiazol-5-yl)benzyl)carbamoyl)pyrrolidin-1-yl)-3,3-dimethyl-1-oxobutan-2-yl)-3,8,13,18-tetraoxaicosanediamide(125)

Compound 125 was prepared accordingly to general method F, starting fromcompound 7 (20 mg, 0.0428 mmol) and compound 103 (7.1 mg, 0.02038 mmol).6.7 mg were obtained (yield: 28%).

¹H-NMR (500 MHz, MeOD) δ: 8.77 (s, 2H), 7.34 (dd, J=8.3, 23.6 Hz, 8H),4.59 (d, J=12.0 Hz, 2H), 4.50-4.40 (m, 6H), 4.26 (dd, J=4.9, 15.9 Hz,2H), 3.86 (dd, J=15.3, 23.4 Hz, 4H), 3.77 (d, J=11.4 Hz, 2H), 3.70 (dd,J=3.9, 11.1 Hz, 2H), 3.46 (t, J=6.0 Hz, 4H), 3.38-3.28 (m, 8H), 2.37 (s,6H), 2.16-2.10 (m, 2H), 2.02-1.96 (m, 2H), 1.62-1.52 (m, 8H), 1.51-1.45(m, 4H), 0.93 (s, 18H).

¹³C-NMR (101 MHz, MeOD) δ: 174.3, 172.1, 172.0, 171.7, 152.8, 149.1,140.3, 133.4, 131.5, 130.5, 130.4, 129.5, 129.0, 72.7, 71.7, 71.5, 71.1,70.7, 60.8, 58.1, 58.0, 43.7, 39.0, 37.2, 27.6, 27.5, 27.4, 15.9.

HRMS: found 1175.6623 [M+H⁺].

N1,N19-Bis((S)-1-((2S,4R)-4-hydroxy-2-((4-(4-methylthiazol-5-yl)benzyl)carbamoyl)pyrrolidin-1-yl)-3,3-dimethyl-1-oxobutan-2-yl)-3,7,13,17-tetraoxanonadecanediamide(126)

Compound 126 was prepared accordingly to general method F, starting fromcompound 7 (20 mg, 0.0428 mmol) and compound 112 (6.8 mg, 0.0204 mmol).6.6 mg were obtained as a white solid (yield: 28%).

¹H-NMR (500 MHz, MeOD) δ: 8.76 (s, 2H), 7.37-7.30 (m, 8H), 4.60 (d,J=9.4 Hz, 2H), 4.50-4.24 (m, 8H), 3.87 (d, J=6.5 Hz, 4H), 3.77 (d,J=11.2 Hz, 2H), 3.70 (dd, J=3.8, 11.5 Hz, 2H), 3.55-3.49 (m, 4H), 3.43(dt, J=1.2, 6.2 Hz, 4H), 3.33-3.29 (m, 4H), 2.37 (s, 6H), 2.16-2.10 (m,2H), 2.03-1.96 (m, 2H), 1.80-1.74 (m, 4H), 1.47-1.40 (m, 4H), 1.30-1.23(m, 2H), 0.93 (s, 18H).

¹³C-NMR (101 MHz, MeOD) δ: 174.3, 171.8, 171.6, 152.8, 149.0, 140.2,133.4, 131.5, 130.5, 130.3, 129.5, 128.9, 71.9, 71.0, 70.8, 69.8, 68.3,60.8, 58.1, 57.9, 43.7, 38.9, 37.2, 30.9, 30.5, 26.9, 23.9, 15.8.

HRMS: found 1161.6446 [M+H⁺].

N1,N21-Bis((S)-1-((2S,4R)-4-hydroxy-2-((4-(4-methylthiazol-5-yl)benzyl)carbamoyl)pyrrolidin-1-yl)-3,3-dimethyl-1-oxobutan-2-yl)-3,6,10,15,19-pentaoxahenicosanediamide(128)

Compound 128 was prepared accordingly to general method F, starting fromcompound 7 (20 mg, 0.0428 mmol) and compound 123 (7.5 mg, 0.02038 mmol).6.5 mg were obtained as a white solid (yield: 27%).

¹H-NMR (500 MHz, MeOD) δ: 9.00 (d, J=1.1 Hz, 2H), 7.45 (dd, J=8.4, 23.1Hz, 8H), 4.71-4.68 (m, 2H), 4.55 (tt, J=12.4, 11.9 Hz, 6H), 4.36 (d,J=15.5 Hz, 2H), 4.03 (d, J=3.6 Hz, 2H), 3.97 (d, J=5.9 Hz, 2H),3.89-3.78 (m, 4H), 3.71-3.68 (m, 2H), 3.64-3.36 (m, 14H), 2.49 (s, 6H),2.26-2.19 (m, 2H), 2.13-2.06 (m, 2H), 1.90-1.84 (m, 2H), 1.85-1.79 (m,2H), 1.61-1.55 (m, 4H), 1.04 (d, J=3.4 Hz, 18H).

¹³C-NMR (101 MHz, MeOD) δ: 174.4, 174.3, 172.1, 171.9, 171.8, 171.7,153.3, 140.6, 131.1, 130.4, 129.0, 72.3, 71.8, 71.2, 71.1, 70.9, 69.9,69.4, 68.7, 68.4, 60.8, 58.2, 58.1, 58.0, 43.7, 38.9, 37.2, 37.1, 31.1,31.0, 27.5, 27.0, 15.4. HRMS: found 1191.6137 [M+H⁺].

(S)-1-((2R,3R,4S)-3-Fluoro-4-hydroxy-2-((4-(4-methylthiazol-5-yl)benzyl)carbamoyl)pyrrolidin-1-yl)-3,3-dimethyl-1-oxobutan-2-aminiumchloride (129)

Compound 129 was prepared accordingly to PATENT WO 2018/051107 A1.Analytical data matched those previously reported.

N1,N20-Bis((S)-1-((2R,3R,4S)-3-fluoro-4-hydroxy-2-((4-(4-methylthiazol-5-yl)benzyl)carbamoyl)pyrrolidin-1-yl)-3,3-dimethyl-1-oxobutan-2-yl)-3,6,9,12,15,18-hexaoxaicosanediamide(130)

Prepared accordingly to general method F, starting from compound 129(16.9 mg, 0.0348 mmol) and 3,6,9,12,15,18-hexaoxaicosanedioic acid (6.17mg, 0.0174 mmol). Obtained 7.5 mg (35% yield) as white solid.

¹H-NMR (400 MHz, MeOD) δ: 8.89 (s, 2), 7.46 (d, J=8.7 Hz, 8H), 4.99 (td,J=3.3, 52.9 Hz, 2H), 4.69 (s, 2H), 4.65 (dd, J=2.9, 21.3 Hz, 2H),4.60-4.34 (m, 6H), 4.08-4.03 (m, 6H), 3.77-3.59 (m, 22H), 2.49 (s, 6H),1.06 (s, 18H).

¹⁹F-NMR (376.45 MHz, MeOD): −201.87 ,¹³C-NMR (101 MHz, MeOD) δ: 170.9,170.5, 169.2, 169.1, 151.5, 147.7, 138.6, 130.2, 129.0, 127.5, 94.0,92.1, 70.9, 70.2, 70.1, 70.1, 69.6, 69.5, 64.4, 64.1, 56.1, 50.9, 42.4,35.3, 25.5, 14.4. HRMS: found 1215.5214 [M+H⁺].

Abbreviations

BAIB, bis-acetoxy iodobenzene;

CID, chemical inducer of dimerization;

CRL, Cullin RING ligase;

DC50, half-degrading concentration;

DCM, dichloromethane;

DIPEA, N,N-Diisopropyethylamine;

DMF, dimethylformamide;

DMSO, dimethylsulfoxide;

HATU, 1-[Bis(dimethylamino)methylene]-1H-1,2,3Ytriazolo[4,5-b]pyridinium3-oxid hexafluorophosphate;

Hdy-HIF-1α, hydroxylated form of HIF-1α;

HIF-1α, hypoxia inducible factor alpha;

Hyp, hydroxyproline;

HOAT, 1-Hydroxy-7-azabenzotriazole;

IAPS, inhibitor of apoptosis proteins;

ITC, isothermal titration calorimetry;

LHS, left hand side;

PEG, polyethylene glycol;

PHD, prolyl hydroxylase domain-containing protein;

PPI, protein-protein interaction;

PROTACS, Proteoysis-Targeting Chimeras;

RHS, right end side;

SEC, size exclusion chromatography;

TEMPO, 2,2,6,6-Tetramethylpiperidin-1-yl)oxyl or(2,2,6,6-tetramethylpiperidin-1-yl)oxidanyl;

TFA, trifluoroacetic acid;

VHL , von Hippel-Lindau;

HRE, hypoxia response element.

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1. A compound having the structure:A-L-B wherein A and B are independently an E3 ubiquitin ligase proteinbinding ligand compound of formula 1A or 1B and at least one of A or Bis the compound of formula 1B:

wherein L is a linking group which is directly bonded to the compound offormula 1A at R¹ or R², and/or directly bonded to the compound offormula 1B at R³ or R⁴ and wherein L is —R⁵—[O(CH₂)_(m)]_(n)—R⁶—,wherein m and n are independently 0 to 10, and R⁵ and R⁶ areindependently selected from the group: covalent bond, C1-C10 alkylene,—OR⁷—, C1-C10 polyether, or —O—; wherein R¹ is selected from either thegroup: (1) a covalent bond, or C1-C5 alkylene when L is bonded to thecompound of formula 1A at R¹, or the group (2) H, NH₂, C1-C5 alkyl, orC(CN)C₂H₄ when L is bonded to the compound of formula 1A at R²; whereinR², R³, and R⁴ are independently selected from the group: a covalentbond, H, NH₂, C1-C5 alkyl, C(CN)C₂H₄; wherein X and Y are independentlyselected from the group: H, OH or halogen; and wherein R⁷ is C1-C5alkylene, or a pharmaceutically acceptable salt, hydrate, solvate orpolymorph thereof.
 2. A compound according to claim 1, wherein X is H orhalogen.
 3. A compound according to claim 1, wherein Y is OH.
 4. Acompound according to claim 1, wherein either A or B is a compoundaccording to formula 1A, wherein A has the formula 1C:


5. A compound according to claim 1, wherein A is a compound of formula1A and B is a compound of formula 1B.
 6. A compound according to claim1, wherein L is connected to A via R¹ of formula 1A.
 7. A compoundaccording to claim 1, wherein L is connected to B via R¹ of formula 1A.8. A compound according to claim 1, wherein R⁵ is a chemical bond, R⁶ isa chemical bond, m is 2 and n is 3, 4 or
 5. 9. A compound according toclaim 8, wherein n is
 5. 10. A compound according to claim 1, whereinthe linker L is a linear chain of 12-20 atoms in length.
 11. A compoundaccording to claim 10, wherein the linker chain comprises carbon and/oroxygen atoms.
 12. A compound according to claim 11, wherein the linkerchain comprises alkylene groups and/or ether groups and/or polyethergroups.
 13. A pharmaceutical composition comprising one or morecompounds according to claim 1 and a pharmaceutically acceptable vehicleor diluent therefor.
 14. A method of use of a compound according toclaim 1 for the treatment of at least one of anaemia due to chronickidney disease, anaemia due to cancer chemotherapy, ischemia, ischemicreperfusion injuries, myocardial infarction, stroke, acute lung injury,intestinal inflammation, wound healing and post-transplantationcomplications, mitochondrial respiratory chain dysfunctions andoncological conditions treatable by enhancing T-cell responses.
 15. Amethod of regulating activity of a target protein in a subjectcomprising administering to said subject an effective amount of acompound according to claim
 1. 16. The method according to claim 15,wherein the target protein is an E3 ubiquitin ligase protein.